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
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
2000
Methanococcus jannaschii Prolyl-Cysteinyl-tRNA Synthetase Possesses Overlapping Amino Acid Binding Sites †
Stathopoulos C, Jacquin-Becker C, Becker H, Li T, Ambrogelly A, Longman R, Söll D. Methanococcus jannaschii Prolyl-Cysteinyl-tRNA Synthetase Possesses Overlapping Amino Acid Binding Sites †. Biochemistry 2000, 40: 46-52. PMID: 11141055, DOI: 10.1021/bi002108x.Peer-Reviewed Original ResearchConceptsAmino acidsTRNA synthetaseProtein translation apparatusCysteinyl-tRNA synthetase activityCognate tRNA speciesSite-directed mutagenesisAmino acid activationAbsence of tRNAAmino acid residuesSynthetase activityTranslation apparatusMethanococcus jannaschiiTRNA speciesCysteine activationUnusual enzymeDifferent amino acidsMutant enzymesCysteine bindingProline bindingProlyl-tRNA synthetase activityAcid residuesAminoacyl-tRNAPosition 103Single enzymeA dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia
Bunjun S, Stathopoulos C, Graham D, Min B, Kitabatake M, Wang A, Wang C, Vivarès C, Weiss L, Söll D. A dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 12997-13002. PMID: 11078517, PMCID: PMC27167, DOI: 10.1073/pnas.230444397.Peer-Reviewed Original ResearchConceptsCys-tRNAAminoacyl-tRNA synthetaseProlyl-tRNA synthetasePrimitive eukaryote Giardia lambliaPro geneEukaryote Giardia lambliaNumber of archaeaAlanyl-tRNA synthetasesCysteinyl-tRNA synthetaseE. coli tRNACysS genesM. jannaschiiMethanococcus jannaschiiMost organismsGenomic sequencesSaccharomyces cerevisiaeCysteinyl-tRNAGene productsPro-tRNATRNA synthetaseDual specificityMethanobacterium thermoautotrophicumProtein synthesisEscherichia coliAmino acidsOne Polypeptide with Two Aminoacyl-tRNA Synthetase Activities
Stathopoulos C, Li T, Longman R, Vothknecht U, Becker H, Ibba M, Söll D. One Polypeptide with Two Aminoacyl-tRNA Synthetase Activities. Science 2000, 287: 479-482. PMID: 10642548, DOI: 10.1126/science.287.5452.479.Peer-Reviewed Original ResearchConceptsProlyl-tRNA synthetaseProtein synthesisCysteinyl-tRNA synthetase activityAmino-terminal sequenceSynthetase activityAminoacyl-tRNA synthetase activityCertain archaeaEvolutionary originMethanococcus jannaschiiGenome sequenceSubstrate specificityGenetic analysisSuch organismsMessenger RNARNA synthetasesSynthetaseSequenceArchaeaJannaschiiSynthetasesRNAOrganismsPolypeptideProlylProteinCysteine Biosynthesis Pathway in the ArchaeonMethanosarcina barkeri Encoded by Acquired Bacterial Genes?
Kitabatake M, So M, Tumbula D, Söll D. Cysteine Biosynthesis Pathway in the ArchaeonMethanosarcina barkeri Encoded by Acquired Bacterial Genes? Journal Of Bacteriology 2000, 182: 143-145. PMID: 10613873, PMCID: PMC94250, DOI: 10.1128/jb.182.1.143-145.2000.Peer-Reviewed Original ResearchConceptsCysteine biosynthesis pathwayCysK geneCysteine biosynthesisBiosynthesis pathwayRecent genome dataOpen reading framePyrococcus sppCysE geneBacterial genesMethanococcus jannaschiiGenome dataArchaeoglobus fulgidusReading frameSulfolobus solfataricusThermoplasma acidophilumCysM geneMethanobacterium thermoautotrophicumGenesBiosynthesisPathwayGreat similaritySame functionCysKOrthologsArchaea
1999
Cysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis
Li T, Graham D, Stathopoulos C, Haney P, Kim H, Vothknecht U, Kitabatake M, Hong K, Eggertsson G, Curnow A, Lin W, Celic I, Whitman W, Söll D. Cysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis. FEBS Letters 1999, 462: 302-306. PMID: 10622715, DOI: 10.1016/s0014-5793(99)01550-1.Peer-Reviewed Original ResearchConceptsLateral gene transferAminoacyl-tRNA synthesisCysteinyl-tRNA synthetaseEscherichia coli cysteinyl-tRNA synthetaseMolecular phylogenyPyrococcus sppMethanococcus jannaschiiMethanococcus maripaludisM. maripaludisMethanogenic archaeaMethanosarcina sppGene transferCysRSMethanosarcina barkeriGenesSpecific relativeLast puzzleSppOrthologsArchaeaPhylogenyJannaschiiMutantsLineagesOrganismsArchaeal Aminoacyl-tRNA Synthesis: Diversity Replaces Dogma
Tumbula D, Vothknecht U, Kim H, Ibba M, Min B, Li T, Pelaschier J, Stathopoulos C, Becker H, Söll D. Archaeal Aminoacyl-tRNA Synthesis: Diversity Replaces Dogma. Genetics 1999, 152: 1269-1276. PMID: 10430557, PMCID: PMC1460689, DOI: 10.1093/genetics/152.4.1269.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisGene transfer eventsPhenylalanyl-tRNA synthetasesLysyl-tRNA synthetaseTransamidation pathwayExtant organismsMethanococcus jannaschiiAsparaginyl-tRNAProtein biosynthesisGenetic codeGene expressionGenome sequencingAminoacyl-tRNAArchaeaMethanobacterium thermoautotrophicumMolecular biologyUnexpected levelNovel pathwayTransfer eventsFaithful translationPathwayJannaschiiSynthetasesBiosynthesisOrganisms
1998
Sequence Divergence of Seryl-tRNA Synthetases in Archaea
Kim H, Vothknecht U, Hedderich R, Celic I, Söll D. Sequence Divergence of Seryl-tRNA Synthetases in Archaea. Journal Of Bacteriology 1998, 180: 6446-6449. PMID: 9851985, PMCID: PMC107743, DOI: 10.1128/jb.180.24.6446-6449.1998.Peer-Reviewed Original ResearchConceptsOpen reading frameM. thermoautotrophicumRelevant open reading frameSeryl-tRNA synthetasesCys-tRNACysCanonical cysteinyl-tRNA synthetaseGel shift experimentsCysteinyl-tRNA synthetaseN-terminal peptide sequenceEscherichia coli tRNASequence divergenceDirect aminoacylationM. jannaschiiMethanococcus jannaschiiGenomic sequencesReading frameSer geneHomologous tRNAsGenomic dataMethanogenic archaeaMethanobacterium thermoautotrophicumShift experimentsEnzymatic propertiesArchaeaSerine
1997
A Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases
Ibba M, Morgan S, Curnow A, Pridmore D, Vothknecht U, Gardner W, Lin W, Woese C, Söll D. A Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases. Science 1997, 278: 1119-1122. PMID: 9353192, DOI: 10.1126/science.278.5340.1119.Peer-Reviewed Original ResearchConceptsClass I aminoacyl-tRNA synthetaseCrenarchaeote Sulfolobus solfataricusDinucleotide-binding domainAminoacyl-tRNA synthetasesAmino acid motifsAmino acid sequenceAminoacyl-tRNA synthetaseLysyl-tRNA synthetaseClass II synthetasesEuryarchaeal genomesUnassigned functionMethanococcus jannaschiiMethanococcus maripaludisLysRS proteinsReading frameSulfolobus solfataricusAcid motifAcid sequenceSuch organismsMethanobacterium thermoautotrophicumLysRSProteinSynthetasesSynthetaseRNA synthetase