2023
Mistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann D, Fischer J, Bile J, Gaier S, Shelley B, Awawdeh A, Jahn M, Hoffman K, Westhof E, Söll D, Clarke C, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. Journal Of Biological Chemistry 2023, 299: 104852. PMID: 37224963, PMCID: PMC10404621, DOI: 10.1016/j.jbc.2023.104852.Peer-Reviewed Original ResearchConceptsTransfer RNAsAmino acidsBacterial transfer RNAsUnfavorable environmental conditionsProlyl-tRNA synthetaseWrong amino acidPoor substrate specificitySubstrate discriminationGrowth defectTransfer RNAGenetic codePosttranslational modificationsProtein reporterTranslation factorsEnvironmental stressFunctional proteinsSubstrate specificityThreonine codonGenetic informationDistinct isoformsPro mutationAntibiotic carbenicillinEscherichia coliNovel familyEnvironmental conditions
2022
Ancestral archaea expanded the genetic code with pyrrolysine
Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O’Donoghue P, Söll D, Tharp JM. Ancestral archaea expanded the genetic code with pyrrolysine. Journal Of Biological Chemistry 2022, 298: 102521. PMID: 36152750, PMCID: PMC9630628, DOI: 10.1016/j.jbc.2022.102521.Peer-Reviewed Original ResearchConceptsAminoacylation efficiencyGenetic code expansionDomains of lifePyrrolysyl-tRNA synthetaseTRNA-binding domainFull-length enzymeNoncanonical amino acidsAmino acid substratesMolecular phylogenyDiverse archaeaCoevolutionary historyTRNA sequencesGenetic codeCode expansionDiscriminator basesMethanogenic archaeaMethanosarcina mazeiPylRSSubstrate spectrumTRNAArchaeaMultiple organismsLiving cellsAcid substratesAmino acidsThe tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism
Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Research 2022, 50: gkac271-. PMID: 35466371, PMCID: PMC9071458, DOI: 10.1093/nar/gkac271.Peer-Reviewed Original ResearchConceptsGenetic code expansionCode expansionDistinct non-canonical amino acidsOrthogonal aminoacyl-tRNA synthetase/tRNA pairsAminoacyl-tRNA synthetase/tRNA pairsPyrrolysyl-tRNA synthetase/Halophilic archaeon Haloferax volcaniiAdditional coding capacityDistinct noncanonical amino acidsNon-canonical amino acidsArchaeon Haloferax volcaniiDiscriminator baseAmino acidsPyrrolysyl-tRNA synthetaseNoncanonical amino acidsSite-specific incorporationMotif 2 loopSingle base changeDistinct tRNAsTRNA pairsHaloferax volcaniiUAA codonGenetic codeDiscriminator basesTRNA structureMeasuring 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 ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnticodonCodonEscherichia coliGenetic CodeProtein BiosynthesisRNA, TransferConceptsFour-base codonsGenetic codeTRNA mutationsAminoacyl-tRNA synthetasesQuadruplet codonsSingle amino acidCodon translationTriplet codonsTRNA synthetasesSynthetic biologistsCodonTRNAAmino acidsChemical alphabetsMutationsMass spectrometrySynthetasesAnticodonToleranceSynthetic systemsBiologistsTranslationEscherichiaNascent
2015
Overcoming Challenges in Engineering the Genetic Code
Lajoie M, Söll D, Church G. Overcoming Challenges in Engineering the Genetic Code. Journal Of Molecular Biology 2015, 428: 1004-1021. PMID: 26348789, PMCID: PMC4779434, DOI: 10.1016/j.jmb.2015.09.003.Peer-Reviewed Original Research
2013
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 5540-5545. PMID: 23509275, PMCID: PMC3619370, DOI: 10.1073/pnas.1303090110.Peer-Reviewed Original ResearchConceptsFrame TGA codonTGA codonGlycine codonHuman microbiotaSingle-cell genome sequencesSmall subunit rRNA sequencesComparative genomic analysisHorizontal gene transferUnique genetic codeGlycyl-tRNA synthetaseHuman Microbiome Project dataStrain-specific variationMost genesSuch taxaBisphosphate carboxylaseGenome sequenceGenetic codeGenomic analysisStriking diversityRRNA sequencesΒ-galactosidase activityGlycine residueStop codonCodonLacZ gene
2008
Quality 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 synthesis: Twenty three amino acids and counting
Ibba M, Stathopoulos C, Söll D. Protein synthesis: Twenty three amino acids and counting. Current Biology 2001, 11: r563-r565. PMID: 11509255, DOI: 10.1016/s0960-9822(01)00344-x.Peer-Reviewed Original Research
2000
Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process
Woese C, Olsen G, Ibba M, Söll D. Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process. Microbiology And Molecular Biology Reviews 2000, 64: 202-236. PMID: 10704480, PMCID: PMC98992, DOI: 10.1128/mmbr.64.1.202-236.2000.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsAmino Acyl-tRNA SynthetasesArchaeaChlorobiEvolution, MolecularGenetic CodePhylogenySpirochaetaThermusConceptsAminoacyl-tRNA synthetasesIndividual aminoacyl-tRNA synthetasesEvolutionary processesAAR geneEvolutionary relationshipsPhylogenetic treeGenetic codeUniversal phylogenetic treeDistant evolutionary pastOrganismal phylogenyOrganismal domainsCodon assignmentsTaxonomic distributionEvolutionary pastHorizontal transferEvolutionary profilesGenetic materialIndividual enzymesEvolutionary perspectiveSynthetasesGenesEnzymeBacteriaModern counterpartsTrees
1999
Archaeal aminoacyl-tRNA synthesis: unique determinants of a universal genetic code?
Ibba M, Curnow A, Bono J, Rosa P, Woese C, Söll D. Archaeal aminoacyl-tRNA synthesis: unique determinants of a universal genetic code? Biological Bulletin 1999, 196: 335-6; discussion 336-7. PMID: 10390832, DOI: 10.2307/1542964.Peer-Reviewed Original Research
1995
Divergence of glutamate and glutamine aminoacylation pathways: Providing the evolutionary rationale for mischarging
Rogers K, Söll D. Divergence of glutamate and glutamine aminoacylation pathways: Providing the evolutionary rationale for mischarging. Journal Of Molecular Evolution 1995, 40: 476-481. PMID: 7783222, DOI: 10.1007/bf00166615.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseGlutamine tRNAEukaryotic organismsProkaryotic organismsGln-tRNAGlnHorizontal gene transfer eventsGene transfer eventsGlutaminyl-tRNA synthetasesGram-negative eubacteriaGlutamyl-tRNA synthetaseAminoacyl-tRNA synthetasesAminoacyl-tRNA synthetaseFamily of enzymesEukaryotic organellesPool of glutamateAminoacyl-tRNATRNADifferent cellular mechanismsEvolutionary rationaleProtein synthesisOrganismsAmino acidsTransfer eventsCellular mechanismsSynthetase
1990
The accuracy of aminoacylation — ensuring the fidelity of the genetic code
Söll D. The accuracy of aminoacylation — ensuring the fidelity of the genetic code. Cellular And Molecular Life Sciences 1990, 46: 1089-1096. PMID: 2253707, DOI: 10.1007/bf01936918.Peer-Reviewed Original ResearchConceptsAccuracy of aminoacylationTransfer RNA speciesAminoacyl-tRNA synthetasesMessenger RNA codonRNA speciesProtein biosynthesisGenetic codeProtein interactionsParticular tRNATRNACorrect attachmentBiophysical techniquesRNA codonsAmino acidsSynthetasesSpecific recognitionProper interactionAnticodonBiosynthesisCodonAminoacylationNucleotidesSpeciesEnzymeIdentity element
1981
A conversational system for the computer analysis of nucleic acid sequences
Sege R, Söll D, Ruddle F, Queen C. A conversational system for the computer analysis of nucleic acid sequences. Nucleic Acids Research 1981, 9: 437-444. PMID: 6163137, PMCID: PMC326703, DOI: 10.1093/nar/9.2.437.Peer-Reviewed Original Research
1976
Studies of the complex between transfer RNAs with complementary anticodons I. Origins of enhanced affinity between complementary triplets
Grosjean H, Söll D, Crothers D. Studies of the complex between transfer RNAs with complementary anticodons I. Origins of enhanced affinity between complementary triplets. Journal Of Molecular Biology 1976, 103: 499-519. PMID: 781277, DOI: 10.1016/0022-2836(76)90214-x.Peer-Reviewed Original Research
1972
Is There a Discriminator Site in Transfer RNA?
Crothers D, Seno T, Söll D. Is There a Discriminator Site in Transfer RNA? Proceedings Of The National Academy Of Sciences Of The United States Of America 1972, 69: 3063-3067. PMID: 4562753, PMCID: PMC389707, DOI: 10.1073/pnas.69.10.3063.Peer-Reviewed Original Research
1971
Purification of Five Leucine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Heterologous Leucyl-Transfer Ribonucleic Acid Synthetase
Blank H, Söll D. Purification of Five Leucine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Heterologous Leucyl-Transfer Ribonucleic Acid Synthetase. Journal Of Biological Chemistry 1971, 246: 4947-4950. PMID: 4936719, DOI: 10.1016/s0021-9258(18)61954-4.Peer-Reviewed Original ResearchMeSH KeywordsAcylationBase SequenceBenzoatesCarbon IsotopesCarcinomaCell LineChromatography, DEAE-CelluloseChromatography, GelDrug StabilityEscherichia coliGenetic CodeHot TemperatureKineticsLeucineLigasesMouth NeoplasmsNucleic Acid DenaturationPolynucleotidesRibosomesRNA, BacterialRNA, TransferTemplates, GeneticYeastsEnzymatic Modification of Transfer RNA
Söll D. Enzymatic Modification of Transfer RNA. Science 1971, 173: 293-299. PMID: 4934576, DOI: 10.1126/science.173.3994.293.Peer-Reviewed Original ResearchConceptsTRNA-modifying enzymesTRNA moleculesTRNA genesTransfer RNAAmino acid biosynthesisParticular tRNA speciesNucleic acid-protein interactionsAminoacyl-tRNA synthetaseSimple selection procedureAmino acid acceptorPrecursor tRNAsActive tRNAMature tRNACellular processesTRNA speciesRegulatory mutantsAcid biosynthesisRNA precursorsProtein factorsIsoacceptor tRNAsDifferent amino acidsNucleotide sequencePolynucleotide levelBiological functionsTRNA
1970
In Vitro Biosynthesis of Pseudouridine at the Polynucleotide Level by an Enzyme Extract from Escherichia coli
Johnson L, Söll D. In Vitro Biosynthesis of Pseudouridine at the Polynucleotide Level by an Enzyme Extract from Escherichia coli. Proceedings Of The National Academy Of Sciences Of The United States Of America 1970, 67: 943-950. PMID: 4943184, PMCID: PMC283296, DOI: 10.1073/pnas.67.2.943.Peer-Reviewed Original ResearchConceptsE. coli RNA polymeraseRNA transcription productsColi RNA polymeraseConversion of uridineE. coli extractsTRNA genesRNA polymerasePolynucleotide levelUridine residuesTranscription productsVitro BiosynthesisMycoplasma spEscherichia coliLambda DNARNADNAMacromolecular levelEnzyme extractBiosynthesisGenesPolymerasePseudouridineSpColiResiduesPurification of Five Serine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Homologous and Heterologous Seryl Transfer Ribonucleic Acid Synthetases
Roy K, Söll D. Purification of Five Serine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Homologous and Heterologous Seryl Transfer Ribonucleic Acid Synthetases. Journal Of Biological Chemistry 1970, 245: 1394-1400. PMID: 4910052, DOI: 10.1016/s0021-9258(18)63249-1.Peer-Reviewed Original Research
1969
CYTOKININS: DISTRIBUTION IN TRANSFER RNA SPECIES OF Escherichia coli*
Armstrong D, Burrows W, Skoog F, Roy K, Söll D. CYTOKININS: DISTRIBUTION IN TRANSFER RNA SPECIES OF Escherichia coli*. Proceedings Of The National Academy Of Sciences Of The United States Of America 1969, 63: 834-841. PMID: 4899879, PMCID: PMC223528, DOI: 10.1073/pnas.63.3.834.Peer-Reviewed Original Research