2008
Life without RNase P
Randau L, Schröder I, Söll D. Life without RNase P. Nature 2008, 453: 120-123. PMID: 18451863, DOI: 10.1038/nature06833.Peer-Reviewed Original Research
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
2002
A one‐step method for in vitro production of tRNA transcripts
Korencić D, Söll D, Ambrogelly A. A one‐step method for in vitro production of tRNA transcripts. Nucleic Acids Research 2002, 30: e105-e105. PMID: 12384607, PMCID: PMC137149, DOI: 10.1093/nar/gnf104.Peer-Reviewed Original ResearchMeSH KeywordsDNADNA-Directed RNA PolymerasesDNA, Single-StrandedGenetic TechniquesRNA, TransferTemplates, GeneticTranscription, GeneticViral ProteinsConceptsTRNA transcriptsT7 RNA polymeraseLarge-scale plasmid preparationTRNA genesMicrobial genomesTRNA functionsDNA promoterRNA polymeraseRNA moleculesT7 promoterBiochemical characterizationTranscription templateDNA templateNew enzymeTranscriptsLarge oligonucleotidesTranscriptionGood substratePromoterShort oligonucleotidesEnzymatic digestionRapid productionPlasmid preparationsGenomeOligonucleotide
1999
Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement
Ibba M, Losey H, Kawarabayasi Y, Kikuchi H, Bunjun S, Söll D. Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 418-423. PMID: 9892648, PMCID: PMC15151, DOI: 10.1073/pnas.96.2.418.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBase SequenceBorrelia burgdorferi GroupCloning, MolecularDiphosphatesEscherichia coliEvolution, MolecularGenes, ArchaealGenes, BacterialGenetic Complementation TestKineticsLysine-tRNA LigaseMethanococcusMolecular Sequence DataNucleic Acid ConformationPhylogenyRNA, Transfer, Amino AcylSequence Analysis, DNASubstrate SpecificityTranscription, GeneticConceptsClass II LysRSAminoacyl-tRNA synthetasesLysyl-tRNA synthetasesSubstrate recognitionMolecular basisBacterial class IClass II enzymesSequence-specific recognitionGene displacementTranslational apparatusTRNA recognitionEscherichia coli strainsLysRSLysRSsSame nucleotideSynthetasesDiscriminator baseUnrelated typesLysine activationCertain bacteriaII enzymesColi strainsTRNALysClass IEnzyme
1998
Major 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
1996
Lactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination?
Kim S, Germond J, Pridmore D, Söll D. Lactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination? Journal Of Bacteriology 1996, 178: 2459-2461. PMID: 8636057, PMCID: PMC177964, DOI: 10.1128/jb.178.8.2459-2461.1996.Peer-Reviewed Original ResearchAmino Acid SequenceAmino Acyl-tRNA SynthetasesAspartate-Ammonia LigaseAspartate-tRNA LigaseBase SequenceGene Expression Regulation, BacterialGenes, BacterialGenetic Complementation TestLactobacillusMolecular Sequence DataNucleic Acid ConformationRNA, Transfer, Amino AcylSequence Homology, Amino AcidTerminator Regions, GeneticTranscription, Genetic
1994
Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis.
Ilag L, Kumar A, Söll D. Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis. The Plant Cell 1994, 6: 265-275. PMID: 7908550, PMCID: PMC160432, DOI: 10.1105/tpc.6.2.265.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde OxidoreductasesAmino Acid SequenceAminolevulinic AcidArabidopsisChlorophyllChloroplastsEscherichia coliGene Expression RegulationGenes, PlantGlutamatesGlutamic AcidIntramolecular TransferasesIsomerasesLightMolecular Sequence DataPromoter Regions, GeneticRNA, Transfer, GluSequence Homology, Amino AcidSequence Homology, Nucleic AcidTranscription, GeneticConceptsC5 pathwayAmino acid sequenceHemA proteinChlorophyll biosynthesisGlu-tRNAALA formationAcid sequenceRNA gel blot analysisDeduced amino acid sequenceGlu-tRNA reductaseChloroplasts of plantsGel blot analysisArabidopsis genesFunctional complementationShort intronsCorresponding genesTranscriptional controlFlower tissuesLight regulationExtensive homologyFirst enzymeUniversal precursorReductase geneChlorophyll formationSecond enzyme
1993
A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase.
Sylvers L, Rogers K, Shimizu M, Ohtsuka E, Söll D. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 1993, 32: 3836-41. PMID: 8385989, DOI: 10.1021/bi00066a002.Peer-Reviewed Original ResearchSPL1-1, 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 synthesisNFS1
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
Mono Q chromatography permits recycling of DNA template and purification of RNA transcripts after T7 RNA polymerase reaction
Jahn M, Jahn D, Kumar A, Söll D. Mono Q chromatography permits recycling of DNA template and purification of RNA transcripts after T7 RNA polymerase reaction. Nucleic Acids Research 1991, 19: 2786-2786. PMID: 1710347, PMCID: PMC328209, DOI: 10.1093/nar/19.10.2786.Peer-Reviewed Original ResearchChromatographyDNADNA-Directed RNA PolymerasesRNAT-PhagesTemplates, GeneticTranscription, GeneticViral Proteins
1990
Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis
O'Neill G, Söll D. Expression of the Synechocystis sp. strain PCC 6803 tRNA(Glu) gene provides tRNA for protein and chlorophyll biosynthesis. Journal Of Bacteriology 1990, 172: 6363-6371. PMID: 2121711, PMCID: PMC526821, DOI: 10.1128/jb.172.11.6363-6371.1990.Peer-Reviewed Original ResearchConceptsSynechocystis 6803Synechocystis spFirst anticodon baseStrain PCC 6803Cyanobacterium Synechocystis spTotal tRNA populationAmount of chlorophyllNorthern blot analysisChlorophyll biosynthesisALA biosynthesisPrecursor tRNAsPCC 6803TRNA speciesProtein biosynthesisTRNA populationCellular RNAAminoacylation assaysChlorophyll levelsBiosynthesisAddition of inhibitorsBlot analysisTranslation systemDelta-aminolevulinic acidTRNAChlorophyllYeast suppressor mutations and transfer RNA processing
Nichols M, Willis I, Söll D. Yeast suppressor mutations and transfer RNA processing. Methods In Enzymology 1990, 181: 377-394. PMID: 2199758, DOI: 10.1016/0076-6879(90)81137-j.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBlotting, NorthernChromosomes, FungalGenes, FungalIndicators and ReagentsMolecular Sequence DataMutationNucleic Acid ConformationNucleic Acid HybridizationRNA Polymerase IIIRNA Processing, Post-TranscriptionalRNA, TransferRNA, Transfer, SerSaccharomyces cerevisiaeSuppression, GeneticTranscription FactorsTranscription, GeneticConceptsTRNA genesMature-sized tRNAsRNA processing reactionsPrimer-directed mutagenesisAminoacyl-tRNA synthetaseTransfer RNA moleculesCognate aminoacyl-tRNA synthetaseRNA processingSuppressor mutationsTRNA locusElongation factorProtein biosynthesisRibosomal interactionsRNA moleculesMutant strainStructural proteinsPink coloniesTranscription efficiencyProcessing reactionsProtein synthesisSuppressor functionTRNALow template concentrationsGenesLoci
1989
A selection for mutants of the RNA polymerase III transcription apparatus: PCF1 stimulates transcription of tRNA and 5S RNA genes.
Willis I, Schmidt P, Söll D. A selection for mutants of the RNA polymerase III transcription apparatus: PCF1 stimulates transcription of tRNA and 5S RNA genes. The EMBO Journal 1989, 8: 4281-4288. PMID: 2686985, PMCID: PMC401634, DOI: 10.1002/j.1460-2075.1989.tb08614.x.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCloning, MolecularDNA-Directed RNA PolymerasesGene ExpressionGenes, DominantGenes, FungalKineticsMolecular Sequence DataMutationOligonucleotide ProbesPlasmidsPromoter Regions, GeneticRNA Polymerase IIIRNA, RibosomalRNA, Ribosomal, 5SRNA, TransferSaccharomyces cerevisiaeSaccharomycetalesSchizosaccharomycesSelection, GeneticSuppression, GeneticTemplates, GeneticTranscription, GeneticConceptsTRNA genesMutant strainTranscription of mutantsTranscription of tRNARNA polymerase IIISuppressor tRNA geneDominant mutant geneWild-type strainStable complexesTranscription apparatusRNA genesStable complex formationUpstream geneTRNA suppressorsPositive regulatorSteady-state levelsComplex assemblyGenetic approachesPolymerase IIIGene transcriptionInternal promoterMutant geneTime-course experimentsTranscriptionGenesMultiple Mutations of the First Gene of a Dimeric tRNA Gene Abolish in Vitro tRNA Gene Transcription
Nichols M, Bell J, Klekamp M, Weil P, Söll D. Multiple Mutations of the First Gene of a Dimeric tRNA Gene Abolish in Vitro tRNA Gene Transcription. Journal Of Biological Chemistry 1989, 264: 17084-17090. PMID: 2676999, DOI: 10.1016/s0021-9258(18)71462-2.Peer-Reviewed Original ResearchMeSH KeywordsCloning, MolecularEndopeptidasesMutationPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidRNA Polymerase IIIRNA, FungalRNA, TransferRNA, Transfer, MetRNA, Transfer, SerSaccharomyces cerevisiaeSchizosaccharomycesTranscription Factor TFIIIBTranscription FactorsTranscription Factors, TFIIITranscription, GeneticConceptsMethionine tRNA geneTRNA genesGene transcriptionInitiator methionine tRNA geneRNA polymerase III systemRNA polymerase III transcriptionMutant tRNA genesTRNA gene transcriptionAdditional protein factorsSerine tRNA genePolymerase III transcriptionRNA polymerase IIIICR sequenceTranscription regulationTRNA locusFirst geneExpression initiatesProtein factorsTranscription studiesPolymerase IIINucleotides 8Gene promoterDetectable transcriptsTranscriptionGenesCharacterization 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
1987
The effect of dam methylation on the expression of glnS in E. coli
Plumbridge J, Söll D. The effect of dam methylation on the expression of glnS in E. coli. Biochimie 1987, 69: 539-541. PMID: 2960382, DOI: 10.1016/0300-9084(87)90091-5.Peer-Reviewed Original ResearchCloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae
Weygand-Durasevic I, johnson-Burke D, Söll D. Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae. Nucleic Acids Research 1987, 15: 1887-1904. PMID: 3031581, PMCID: PMC340606, DOI: 10.1093/nar/15.5.1887.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseSingle open reading frameAbundant yeast proteinsGenomic Southern blotsNuclease S1 analysisOpen reading frameTranslation initiation codonAmino acid sequenceKb SalI fragmentNucleotide sequence analysisAT-rich sequencesYeast proteinsStructural geneCodon usageS1 analysisTATA boxInitiation codonReading frameSer geneSalI fragmentAcid sequenceExpression librarySequence analysisRich sequencesSouthern blotSimplified in vitro synthesis of mutated RNA molecules
Krupp G, Söll D. Simplified in vitro synthesis of mutated RNA molecules. FEBS Letters 1987, 212: 271-275. PMID: 3545903, DOI: 10.1016/0014-5793(87)81359-5.Peer-Reviewed Original ResearchSubstrate recognition and identification of splice sites by the tRNA-splicing endonuclease and ligase from Saccharomyces cerevisiae.
Greer C, Söll D, Willis I. Substrate recognition and identification of splice sites by the tRNA-splicing endonuclease and ligase from Saccharomyces cerevisiae. Molecular And Cellular Biology 1987, 7: 76-84. PMID: 3550427, PMCID: PMC365043, DOI: 10.1128/mcb.7.1.76.Peer-Reviewed Original Research