2022
Measuring the tolerance of the genetic code to altered codon size
DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. ELife 2022, 11: e76941. PMID: 35293861, PMCID: PMC9094753, DOI: 10.7554/elife.76941.Peer-Reviewed Original ResearchConceptsFour-base codonsGenetic codeTRNA mutationsAminoacyl-tRNA synthetasesQuadruplet codonsSingle amino acidCodon translationTriplet codonsTRNA synthetasesSynthetic biologistsCodonTRNAAmino acidsChemical alphabetsMutationsMass spectrometrySynthetasesAnticodonToleranceSynthetic systemsBiologistsTranslationEscherichiaNascent
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
2000
Ancient Adaptation of the Active Site of Tryptophanyl-tRNA Synthetase for Tryptophan Binding †
Ibba M, Stange-Thomann N, Kitabatake M, Ali K, Söll I, Carter, C, Michael Ibba, and, Söll D. Ancient Adaptation of the Active Site of Tryptophanyl-tRNA Synthetase for Tryptophan Binding †. Biochemistry 2000, 39: 13136-13143. PMID: 11052665, DOI: 10.1021/bi001512t.Peer-Reviewed Original ResearchMeSH KeywordsAcylationAnimalsBacillus subtilisBacterial ProteinsBinding SitesCattleDiphosphatesDNA Mutational AnalysisDNA, BacterialEvolution, MolecularGeobacillus stearothermophilusHumansKineticsMiceMutagenesis, Site-DirectedProtein BindingRabbitsRNA, Transfer, TrpSequence Homology, Amino AcidTryptophanTryptophan-tRNA LigaseTyrosineConceptsAmino acid specificityActive site residuesTyrosyl-tRNA synthetasesTryptophanyl-tRNA synthetaseAncient adaptationAnalogous residuesGlu side chainsTryptophan replacementHomologous positionsSystematic mutationAromatic side chainsTrpRSTryptophan recognitionBacillus stearothermophilusSide chainsTryptophan bindingTyrRSResiduesCommon originCompetitive inhibitorMutationsTrp bindingMechanistic supportCatalytic efficiencyActive site
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 formsTranscriptsMutationsPathwayEukaryotes
1997
A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene
Kim S, Stange-Thomann N, Martins O, Hong K, Söll D, Fox T. A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene. Journal Of Bacteriology 1997, 179: 5625-5627. PMID: 9287027, PMCID: PMC179443, DOI: 10.1128/jb.179.17.5625-5627.1997.Peer-Reviewed Original ResearchMeSH KeywordsBacillus subtilisDNA, FungalDNA, MitochondrialFungal ProteinsGenes, BacterialMitochondrial ProteinsMolecular Sequence DataProtein BiosynthesisRecombinant Fusion ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Analysis, DNASequence Homology, Amino AcidTransaminasesTranscription Factors
1996
Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase
Kitabatake M, Inokuchi H, Ibba M, Hong K, Söll D. Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase. Molecular Genetics And Genomics 1996, 252: 717-722. PMID: 8917315, DOI: 10.1007/bf02173978.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseWild-type enzymeSubstrate discriminationDouble mutantSubstrate recognition domainThree-dimensional structureAnticodon recognitionSubstrate specificityTRNA bindingGenetic analysisAcceptor stemRecognition domainC171Ternary complexExtensive interactionsMutantsPotential involvementG mutationEnzymeHigh KmSynthetaseMutationsActive siteE222GlnREscherichia coli Tryptophanyl-tRNA Synthetase Mutants Selected for Tryptophan Auxotrophy Implicate the Dimer Interface in Optimizing Amino Acid Binding †
Sever S, Rogers K, Rogers M, Carter C, Söll D. Escherichia coli Tryptophanyl-tRNA Synthetase Mutants Selected for Tryptophan Auxotrophy Implicate the Dimer Interface in Optimizing Amino Acid Binding †. Biochemistry 1996, 35: 32-40. PMID: 8555191, DOI: 10.1021/bi952103d.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacillus subtilisBase SequenceBinding SitesCloning, MolecularDNA PrimersEscherichia coliGenes, BacterialGeobacillus stearothermophilusHaemophilus influenzaeKineticsMacromolecular SubstancesModels, MolecularMolecular Sequence DataPolymerase Chain ReactionProtein FoldingProtein Structure, SecondaryRecombinant ProteinsRestriction MappingSequence Homology, Amino AcidTryptophanTryptophan-tRNA LigaseConceptsTryptophanyl-tRNA synthetaseDimer interfaceClass I aminoacyl-tRNA synthetasesAminoacyl-tRNA synthetasesAmino acid bindingAmino acid activationActive siteSteady-state kinetic analysisSynthetase mutantsRossmann foldApparent KmKMSKS loopTrp lociProtein structureTrpR proteinTryptophan auxotrophDimeric enzymeAuxotrophic strainsBacillus stearothermophilusAcid bindingEscherichia coliOptimal catalysisAminoacyl adenylatesMutantsMutations
1993
SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing
Kolman C, Söll D. SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing. Journal Of Bacteriology 1993, 175: 1433-1442. PMID: 8444805, PMCID: PMC193230, DOI: 10.1128/jb.175.5.1433-1442.1993.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBlotting, NorthernIntronsMolecular Sequence DataMutationNucleic Acid ConformationRNA Processing, Post-TranscriptionalRNA SplicingRNA, FungalRNA, TransferSaccharomyces cerevisiaeSequence Homology, Amino AcidSequence Homology, Nucleic AcidTranscription, GeneticConceptsTRNA genesSaccharomyces cerevisiae genesMature suppressor tRNASuppressor tRNA geneOpen reading frameSaccharomyces cerevisiae mutationsCerevisiae genesTRNA splicingSuppression phenotypeTRNA processingChromosome IIIGenetic approachesSuppressor tRNAReading frameGenetic analysisNorthern analysisMutant selectionMutantsNonsense mutationGenesMutationsLEU2Cell levelIncreased synthesisNFS1The periplasmic dipeptide permease system transports 5-aminolevulinic acid in Escherichia coli
Verkamp E, Backman V, Björnsson J, Söll D, Eggertsson G. The periplasmic dipeptide permease system transports 5-aminolevulinic acid in Escherichia coli. Journal Of Bacteriology 1993, 175: 1452-1456. PMID: 8444807, PMCID: PMC193232, DOI: 10.1128/jb.175.5.1452-1456.1993.Peer-Reviewed Original ResearchConceptsDpp operonE. coli chromosomeEscherichia coliWild-type growthClasses of mutantsAbsence of ALAGenetic screenDpp mutationsColi chromosomeDpp transportALA biosynthesisFirst geneDipeptide transport systemAnaerobic growthChromosomal insertionOperonRecombinant plasmidTransport systemExogenous ALAALA uptakeE. coliNormal growthMutantsMutationsColi
1992
Switching tRNA(Gln) identity from glutamine to tryptophan.
Rogers M, Adachi T, Inokuchi H, Söll D. Switching tRNA(Gln) identity from glutamine to tryptophan. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89: 3463-3467. PMID: 1565639, PMCID: PMC48888, DOI: 10.1073/pnas.89.8.3463.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnticodonBase SequenceBeta-GalactosidaseCloning, MolecularEscherichia coliGenes, BacterialGenes, SuppressorGenes, SyntheticGlutamineMolecular Sequence DataMutagenesis, Site-DirectedNucleic Acid ConformationRNA, Transfer, GlnSuppression, GeneticTetrahydrofolate DehydrogenaseTryptophanConceptsOpal suppressorEscherichia coli glutaminyl-tRNA synthetaseAccuracy of aminoacylationGlutaminyl-tRNA synthetaseN-terminal sequence analysisEfficient suppressorYeast mitochondriaRespective tRNAsUCA anticodonAmber suppressorFol geneUGA codonUGA mutationsSequence analysisAlanine insertionAnticodonGenetic selectionBase pairsBase substitutionsSuppressorTRNATrpRSDihydrofolate reductasePosition 35Mutations
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
Inaccuracy and the Recognition of †RNA
Rogers M, Soll D. Inaccuracy and the Recognition of †RNA. Progress In Nucleic Acid Research And Molecular Biology 1990, 39: 185-208. PMID: 2247608, DOI: 10.1016/s0079-6603(08)60627-3.Peer-Reviewed Original ResearchConceptsATP-dependent stepNoncognate aminoacyl-tRNAsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesRecognition of tRNAAmber mutationGlnRAminoacyl-tRNAEditing mechanismTRNAMutantsMischargingCentral roleEnzymeSynthetasesMisaminoacylationSupF.SupFSynthetaseMutationsGlutamineMechanismSuppressionAssays
1989
Characterization of cis-acting mutations which increase expression of a glnS-lacZ fusion in Escherichia coli
Plumbridge J, Söll D. Characterization of cis-acting mutations which increase expression of a glnS-lacZ fusion in Escherichia coli. Molecular Genetics And Genomics 1989, 216: 113-119. PMID: 2471922, DOI: 10.1007/bf00332238.Peer-Reviewed Original Research
1985
Mutations preventing expression of sup3 tRNASer nonsense suppressors of Schizosaccharomyces pombe.
Pearson D, Willis I, Hottinger H, Bell J, Kumar A, Leupold U, Söll D. Mutations preventing expression of sup3 tRNASer nonsense suppressors of Schizosaccharomyces pombe. Molecular And Cellular Biology 1985, 5: 808-815. PMID: 3921825, PMCID: PMC366785, DOI: 10.1128/mcb.5.4.808.Peer-Reviewed Original ResearchConceptsTRNA genesSchizosaccharomyces pombeGenomic clone bankEucaryotic tRNA genesTranscription control regionsIdentification of mutationsClone bankTRNA precursorsControl regionNonsense codonGenetic evidenceNonsense suppressorsRevertant allelesTranscriptional efficiencySaccharomyces cerevisiae extractSequence analysisSuppressor locusColony hybridizationMutational hotspotsPoint mutationsCerevisiae extractGenesPombeMutationsSplicingMutations Preventing Expression of sup3 tRNASer Nonsense Suppressors of Schizosaccharomyces pombe
Pearson D, Willis I, Hottinger H, Bell J, Kumar A, Leupold U, Söll D. Mutations Preventing Expression of sup3 tRNASer Nonsense Suppressors of Schizosaccharomyces pombe. Molecular And Cellular Biology 1985, 5: 808-815. DOI: 10.1128/mcb.5.4.808-815.1985.Peer-Reviewed Original ResearchTRNA genesGenomic clone bankEucaryotic tRNA genesTranscription control regionsIdentification of mutationsSchizosaccharomyces pombeClone bankTRNA precursorsControl regionNonsense codonGenetic evidenceNonsense suppressorsRevertant allelesTranscriptional efficiencySaccharomyces cerevisiae extractSequence analysisSuppressor locusColony hybridizationMutational hotspotsPoint mutationsCerevisiae extractGenesMutationsSup3SchizosaccharomycesMutations Preventing Expression of sup3 tRNASer Nonsense Suppressors of Schizosaccharomyces pombe
Pearson D, Willis I, Hottinger H, Bell J, Kumar A, Leupold U, Söll D. Mutations Preventing Expression of sup3 tRNASer Nonsense Suppressors of Schizosaccharomyces pombe. Molecular And Cellular Biology 1985, 5: 808-815. DOI: 10.1128/mcb.5.4.808-815.1985.Peer-Reviewed Original ResearchSup3-e geneTRNA genesInternal transcriptional control regionSuppression of nonsense codonsGenomic clone bankEucaryotic tRNA genesSaccharomyces cerevisiae extractsTranscriptional control regionIdentification of mutationsSchizosaccharomyces pombeColony hybridizationRevertant allelesTRNA precursorsClone bankNonsense codonSuppressor locusGenetic evidenceSequence analysisControl regionMutational hotspotsTranscription efficiencyPoint mutationsGenesMutationsSup3Two control systems modulate the level of glutaminyl-tRNA synthetase in Escherichia coli
Cheung A, Watson L, Söll D. Two control systems modulate the level of glutaminyl-tRNA synthetase in Escherichia coli. Journal Of Bacteriology 1985, 161: 212-218. PMID: 2578447, PMCID: PMC214858, DOI: 10.1128/jb.161.1.212-218.1985.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseEscherichia coli glutaminyl-tRNA synthetaseBeta-galactosidase structural genePost-transcriptional regulationStructural geneTranscriptional controlRegulatory mutationsTranslational levelGln-10Metabolic regulationEscherichia coliSynthetaseVivo expressionTranscriptionGrowth conditionsRegulationMRNA levelsRegulatory studiesSynthetase levelsMutationsGlnGrowth rateGenesPromoterColi
1984
Misaminoacylation by glutaminyl-tRNA synthetase: relaxed specificity in wild-type and mutant enzymes.
Hoben P, Uemura H, Yamao F, Cheung A, Swanson R, Sumner-Smith M, Söll D. Misaminoacylation by glutaminyl-tRNA synthetase: relaxed specificity in wild-type and mutant enzymes. The FASEB Journal 1984, 43: 2972-6. PMID: 6389180.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant enzymesWild-type GlnRSAmino-terminal halfAmino acid sequenceAmino acid changesStructural gene mutationsTranslational controlTRNA speciesRelaxed specificityGene sequencesAcid sequenceGlnRRegulation mechanismAcid changesMonomeric polypeptideAmino acidsEnzymeTRNATyrSynthetaseMutationsGene mutationsGlutamineSequenceMisaminoacylationMutations affecting excision of the intron from a eukaryotic dimeric tRNA precursor.
Willis I, Hottinger H, Pearson D, Chisholm V, Leupold U, Söll D. Mutations affecting excision of the intron from a eukaryotic dimeric tRNA precursor. The EMBO Journal 1984, 3: 1573-1580. PMID: 6430697, PMCID: PMC557561, DOI: 10.1002/j.1460-2075.1984.tb02013.x.Peer-Reviewed Original ResearchConceptsTRNA precursorsDimeric tRNA precursorSerine tRNA geneEfficiency of splicingPrecursor tRNA processingSingle base changeTRNA genesTRNASer geneTRNA processingGene transcriptionNucleotide sequenceUGA mutationsD-loopMutant geneGenesBase changesExtra armMutationsIntronsTranscriptionVivo systemDimeric precursorSequenceTRNASerSplicing
1979
Glutamyl-γ-methyl ester acts as a methionine analogue in Escherichia coli: analogue resistant mutants map at the metJ and metK loci
Kraus J, Soll D, Low K. Glutamyl-γ-methyl ester acts as a methionine analogue in Escherichia coli: analogue resistant mutants map at the metJ and metK loci. Genetics Research 1979, 33: 49-55. PMID: 383574, DOI: 10.1017/s0016672300018152.Peer-Reviewed Original Research