2005
RNA-Dependent Cysteine Biosynthesis in Archaea
Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR, Ibba M, Söll D. RNA-Dependent Cysteine Biosynthesis in Archaea. Science 2005, 307: 1969-1972. PMID: 15790858, DOI: 10.1126/science.1108329.Peer-Reviewed Original ResearchConceptsCysteine biosynthesisSep-tRNAComparative genomic analysisCys-tRNA synthasePhosphoseryl-tRNA synthetaseCys-tRNACysteine auxotrophyMost organismsMethanocaldococcus jannaschiiMethanococcus maripaludisGenetic codeGenomic analysisEssential enzymeO-phosphoserineBiosynthesisRNA synthetaseOrganismsSepRSSynthetasePartial purificationCysteineSole routeArchaeaSepCysSJannaschii
2004
Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis
Hendrickson E, Kaul R, Zhou Y, Bovee D, Chapman P, Chung J, de Macario E, Dodsworth J, Gillett W, Graham D, Hackett M, Haydock A, Kang A, Land M, Levy R, Lie T, Major T, Moore B, Porat I, Palmeiri A, Rouse G, Saenphimmachak C, Söll D, Van Dien S, Wang T, Whitman W, Xia Q, Zhang Y, Larimer F, Olson M, Leigh J. Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis. Journal Of Bacteriology 2004, 186: 6956-6969. PMID: 15466049, PMCID: PMC522202, DOI: 10.1128/jb.186.20.6956-6969.2004.Peer-Reviewed Original ResearchMeSH KeywordsArchaeal ProteinsGenome, ArchaealHydrogenMethaneMethanococcusMolecular Sequence DataProteomeSequence Analysis, DNAConceptsProtein-coding genesMethanocaldococcus jannaschiiGenome sequenceSingle circular chromosomeLateral gene transferSelenocysteine-containing proteinsSubunit of enzymeGene lossCircular chromosomeReplication initiationUnique ORFsIron-sulfur centersClose homologMethanococcus maripaludisRNase HIIM. maripaludisRNase HIMethanogenesis enzymesMass spectrometric identificationRedox functionAlanine racemaseAlanine dehydrogenaseGenesGene transferFull complementThe 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
Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis
Stathopoulos C, Kim W, Li T, Anderson I, Deutsch B, Palioura S, Whitman W, Söll D. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 14292-14297. PMID: 11717392, PMCID: PMC64675, DOI: 10.1073/pnas.201540498.Peer-Reviewed Original ResearchConceptsCysteinyl-tRNA synthetaseMethanococcus maripaludisArchaeon Methanococcus maripaludisLateral gene transferNormal growth conditionsAminoacyl-tRNA synthetasesAminoacyl-tRNA synthetaseArchaea Methanocaldococcus jannaschiiProlyl-tRNA synthetaseCysS genesCys-tRNAMethanocaldococcus jannaschiiM. maripaludisSynthetase geneIntriguing enzymeMethanothermobacter thermautotrophicusCysteinyl-tRNAKnockout strainProlyl-tRNAGene transferSynthetaseBiochemical analysisVivo translationGrowth conditionsCysRS
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 enzymeOne 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 synthetasesSynthetaseSequenceArchaeaJannaschiiSynthetasesRNAOrganismsPolypeptideProlylProtein
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 puzzleSppOrthologsArchaeaPhylogenyJannaschiiMutantsLineagesOrganismsSubstrate 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
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