2023
Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids
Jiang H, Weng J, Wang Y, Tsou J, Chen P, Ko A, Söll D, Tsai M, Wang Y. Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Frontiers In Genetics 2023, 14: 1277489. PMID: 37904728, PMCID: PMC10613524, DOI: 10.3389/fgene.2023.1277489.Peer-Reviewed Original ResearchUnique biophysical propertiesTree of lifeAmino acidsSuperfolder green fluorescent proteinGreen fluorescent proteinSubstrate polyspecificityTranslational machinerySynthetic biologistsSmall proteinsFluorescent proteinPhysiological roleRibosomal synthesisProteinBiophysical propertiesKinetic assaysHuman heavy chain ferritinHeavy-chain ferritinPylRSTRNAMutantsAminoacylationPeptidesBiologistsPhysiochemical propertiesMachinery
2022
Diversification of aminoacyl-tRNA synthetase activities via genomic duplication
Krahn N, Söll D, Vargas-Rodriguez O. Diversification of aminoacyl-tRNA synthetase activities via genomic duplication. Frontiers In Physiology 2022, 13: 983245. PMID: 36060688, PMCID: PMC9437257, DOI: 10.3389/fphys.2022.983245.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenomic duplicationSynthetase familyRecent bioinformatic analysisAminoacyl-tRNA synthetase familySynthetic biology applicationsDomains of lifeNew drug targetsAminoacyl-tRNA synthetase activityGene duplicationPhylogenetic diversityEvolutionary eventsGenetic codeBioinformatics analysisImportant bioactive moleculesAdaptive advantageBiological functionsBiological processesBiology applicationsDrug targetsDuplicationAaRSsCatalytic siteSynthetase activityProteinBioactive moleculesKhorana, Har Gobind
Söll D, RajBhandary U. Khorana, Har Gobind. 2022 DOI: 10.1016/b978-0-12-822563-9.00089-5.Peer-Reviewed Original ResearchGene synthesisDNA genesChemical synthesisChemical biologyGenetic codeMembrane proteinsDNA mutagenesisDNA sequencesSynthesis of DNABacterio-opsinG proteinsSuch profound effectsProton pumpMRNA synthesisGenesDNA sequencingBiological researchSynthesisBiologyPCR amplificationDNA chipChemistryNucleic acidsDNA diagnosticsProtein
2020
Front Cover: Hijacking Translation Initiation for Synthetic Biology (ChemBioChem 10/2020)
Tharp J, Krahn N, Varshney U, Söll D. Front Cover: Hijacking Translation Initiation for Synthetic Biology (ChemBioChem 10/2020). ChemBioChem 2020, 21: 1383-1383. DOI: 10.1002/cbic.202000239.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2014
Exploring the Substrate Range of Wild‐Type Aminoacyl‐tRNA Synthetases
Fan C, Ho JM, Chirathivat N, Söll D, Wang Y. Exploring the Substrate Range of Wild‐Type Aminoacyl‐tRNA Synthetases. ChemBioChem 2014, 15: 1805-1809. PMID: 24890918, PMCID: PMC4133344, DOI: 10.1002/cbic.201402083.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesSubstrate rangeDifferent amino acid sitesAmino acidsE. coli tryptophanyl-tRNA synthetaseE. coli aminoacyl-tRNA synthetasesAmino acid sitesCanonical amino acidsNonstandard amino acidsTyrosyl-tRNA synthetaseTryptophanyl-tRNA synthetaseAnticodon sequenceTRNA synthetasesSynthetasesSynthetaseSequenceAnticodonNSAAsTrpRSProteinAminoacylAcid
2013
Back Cover: Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation (Angew. Chem. Int. Ed. 5/2013)
Aldag C, Bröcker M, Hohn M, Prat L, Hammond G, Plummer A, Söll D. Back Cover: Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation (Angew. Chem. Int. Ed. 5/2013). Angewandte Chemie International Edition 2013, 52: 1596-1596. DOI: 10.1002/anie.201300063.Peer-Reviewed Original Research
2008
Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality
Nozawa K, O’Donoghue P, Gundllapalli S, Araiso Y, Ishitani R, Umehara T, Söll D, Nureki O. Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality. Nature 2008, 457: 1163-1167. PMID: 19118381, PMCID: PMC2648862, DOI: 10.1038/nature07611.Peer-Reviewed Original ResearchConceptsAmino acidsMolecular basisLast universal common ancestorUniversal common ancestorUAG stop codonProteinogenic amino acidsCommon ancestorSuppressor tRNAStop codonDesulfitobacterium hafnienseStandard amino acidsTRNADistinct interactionsProteinPyrrolysinePylRSSelenocysteineAncestorCodonMachineryAcidVivoPairsQuality control despite mistranslation caused by an ambiguous genetic code
Ruan B, Palioura S, Sabina J, Marvin-Guy L, Kochhar S, LaRossa RA, Söll D. Quality control despite mistranslation caused by an ambiguous genetic code. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 16502-16507. PMID: 18946032, PMCID: PMC2575449, DOI: 10.1073/pnas.0809179105.Peer-Reviewed Original ResearchConceptsGenetic codeAa-tRNAWild-type proteinAminoacyl-tRNA synthetasesInactive mutant proteinsHeat shock responseE. coliMutant proteinsReporter proteinMissense suppressionFunctional proteinsCognate tRNASelective pressureAminoacyl-tRNAActive enzymeShock responseProtein synthesisNative conformationEnergetic costAmino acidsMissense mutationsProteinBiochemical evidenceCorrect pairingProtein quality
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
A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*
Hamano-Takaku F, Iwama T, Saito-Yano S, Takaku K, Monden Y, Kitabatake M, Söll D, Nishimura S. A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*. Journal Of Biological Chemistry 2000, 275: 40324-40328. PMID: 11006270, DOI: 10.1074/jbc.m003696200.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsTyrosyl-tRNA synthetaseEscherichia coli tyrosyl-tRNA synthetasePosition 130Amino acidsVivo protein biosynthesisE. coli cellsAminoacyl-tRNA formationSingle point mutationTyrRS mutantsCellular proteinsProtein biosynthesisTYR geneMutant enzymesPlasmid libraryReplacement of phenylalanineColi cellsImmense potentialNormal phenotypeEfficient productionPoint mutationsTyrRSProteinPolymerase chain reaction techniqueSynthetaseThe Adaptor hypothesis revisited
Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D, Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D. The Adaptor hypothesis revisited. Trends In Biochemical Sciences 2000, 25: 311-316. PMID: 10871880, DOI: 10.1016/s0968-0004(00)01600-5.Peer-Reviewed Original ResearchOne 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
1998
Maize 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 substrateSynthetaseColiSynthetasesTRNAVivoCDNAMaizeEnzyme
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 synthetaseA 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
Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis
Kumar A, Schaub U, Söll D, Ujwal M. Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis. Trends In Plant Science 1996, 1: 371-376. DOI: 10.1016/s1360-1385(96)80311-6.Peer-Reviewed Original ResearchTransfer RNAConversion of GSAGlu-tRNA reductaseEssential biosynthetic processesVariety of plantsChlorophyll biosynthesisGlu-tRNAHigher plantsProtein biosynthesisBiosynthetic processesBiosynthesisPlantsPivotal stepFirst pivotal stepChloroplastsKey precursorBiosynthesesGenesRNAProteinReductaseChlorophyllEnzymeRegulationAlaHomologous 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 strategyAminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †
Sherman J, Söll D. Aminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †. Biochemistry 1996, 35: 601-607. PMID: 8555233, DOI: 10.1021/bi951602b.Peer-Reviewed Original ResearchConceptsTRNA recognitionNoncognate tRNAsEscherichia coli glutaminyl-tRNA synthetaseWild-type GlnRSGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesNucleic acid interactionsGlutamine tRNAFirst base pairMutational analysisSpecific proteinsTRNAGlnRSequence preferenceMutantsBase pairsAcid interactionsDecreased affinityVivoTRNAGlnAffinitySynthetasesProteinSynthetaseCrystal structure
1994
A 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
1993
Identification of a 100‐kDa protein associated with nuclear ribonuclease P activity in Schizosaccharomyces pombe
ZIMMERLY S, DRAINAS D, SYLVERS L, Dieter S. Identification of a 100‐kDa protein associated with nuclear ribonuclease P activity in Schizosaccharomyces pombe. The FEBS Journal 1993, 217: 501-507. PMID: 8223594, DOI: 10.1111/j.1432-1033.1993.tb18270.x.Peer-Reviewed Original ResearchConceptsFission yeast Schizosaccharomyces pombeYeast Schizosaccharomyces pombeGlycerol gradient fractionationCross-linking experimentsPrecursor tRNAsSchizosaccharomyces pombeRibonuclease PProtein interactsRNA componentProtein componentsP activityRibonuclease P activityApparent homogeneityDEAE-cellulose chromatographyPhosphocellulose chromatographySpecific fashionProtein