2024
Editorial: Synthetic biology and therapeutic applications of transfer RNA
Söll D, O’Donoghue P, Heinemann I. Editorial: Synthetic biology and therapeutic applications of transfer RNA. Frontiers In Genetics 2024, 15: 1468891. PMID: 39205939, PMCID: PMC11349731, DOI: 10.3389/fgene.2024.1468891.Peer-Reviewed Original ResearchReplacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility
Evans R, Krahn N, Weiss J, Vincent K, Söll D, Armstrong F. Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility. Journal Of The American Chemical Society 2024, 146: 16971-16976. PMID: 38747098, PMCID: PMC11212049, DOI: 10.1021/jacs.4c03489.Peer-Reviewed Original ResearchProton-electron transferConcerted proton-coupled electron transferProton-coupled electron transferHydrogen production activityLowest energy pathwayProtein film voltammetryProton affinityReversible electrocatalystsSmall overpotentialProton reductionElectron transferProduction catalystsElectrocatalytic propertiesCysteine ligandsPlatinum metalsFilm voltammetryEnergy pathwaysProtonElectrocatalystsVoltammetryElectrocatalyticallyOverpotentialCatalystTransferCysteineEngineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins
Thaenert A, Sevostyanova A, Chung C, Vargas-Rodriguez O, Melnikov S, Söll D. Engineered mRNA–ribosome fusions for facile biosynthesis of selenoproteins. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321700121. PMID: 38442159, PMCID: PMC10945757, DOI: 10.1073/pnas.2321700121.Peer-Reviewed Original ResearchConceptsSelenocysteine insertion sequenceRibosomal RNARibosome engineeringMessenger RNARegulatory RNA elementsMachinery of protein synthesisInsertion of SecSec-containing proteinsSite-specific insertionBiosynthesis of selenoproteinsNatural messenger RNALive bacterial cellsRNA elementsUAG codonInsertion sequenceRibosome structureUGA codonSec codonInsert SecStop codonSynthetic biologyDesigning proteinsRibosomePolypeptide chainBacterial cellsA novel tRNA feature found in an archaeal pyrrolysyl tRNA is a requirement for PylRS recognition
Zhang J, Krahn N, Melnikov S, Tharp J, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. A novel tRNA feature found in an archaeal pyrrolysyl tRNA is a requirement for PylRS recognition. Biophysical Journal 2024, 123: 181a. DOI: 10.1016/j.bpj.2023.11.1182.Peer-Reviewed Original Research
2023
tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut
Krahn N, Zhang J, Melnikov S, Tharp J, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Research 2023, 52: 513-524. PMID: 38100361, PMCID: PMC10810272, DOI: 10.1093/nar/gkad1188.Peer-Reviewed Original ResearchRational 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 propertiesMachineryCreating Selenocysteine-Specific Reporters Using Inteins
Chung C, Söll D, Krahn N. Creating Selenocysteine-Specific Reporters Using Inteins. Methods In Molecular Biology 2023, 2676: 69-86. PMID: 37277625, DOI: 10.1007/978-1-0716-3251-2_5.Peer-Reviewed Original ResearchRecoding UAG to selenocysteine in Saccharomyces cerevisiae
Hoffman K, Chung C, Mukai T, Krahn N, Jiang H, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA 2023, 29: 1400-1410. PMID: 37279998, PMCID: PMC10573291, DOI: 10.1261/rna.079658.123.Peer-Reviewed Original ResearchConceptsSelenoprotein productionYeast expression systemSeryl-tRNA synthetaseSite-specific incorporationEukaryotic relativesKingdom FungiSelenocysteine synthaseSelenophosphate synthetaseBiosynthesis pathwayEukaryotic selenoproteinsMetabolic engineeringBiosynthetic pathwayPathway componentsExpression systemReductase enzymeTRNASaccharomycesYeastTranslation componentsSpecific sitesFacile productionUnique chemicalSynthetasePathwayFirst demonstrationMistranslation 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 conditionsSplit aminoacyl-tRNA synthetases for proximity-induced stop codon suppression
Jiang H, Ambrose N, Chung C, Wang Y, Söll D, Tharp J. Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2219758120. PMID: 36787361, PMCID: PMC9974479, DOI: 10.1073/pnas.2219758120.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesCodon suppressionStop codon suppressionGene expressionOrthogonal aminoacyl-tRNA synthetasesRelevant protein-protein interactionsSynthetic biology toolsSmall molecule rapamycinControl gene expressionProtein-protein interactionsLevel of transcriptionAbscisic acidDimerization domainMammalian cellsBiology toolsGene translationTranslational levelMolecular switchStop codonHuman cellsMolecular inputsUseful biotechnologySynthetasesExpressionTherapeutic applicationsDual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins
Morosky P, Comyns C, Nunes L, Chung C, Hoffmann P, Söll D, Vargas-Rodriguez O, Krahn N. Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins. Frontiers In Molecular Biosciences 2023, 10: 1096261. PMID: 36762212, PMCID: PMC9902344, DOI: 10.3389/fmolb.2023.1096261.Peer-Reviewed Original ResearchPost-translational modificationsGenetic code expansionAmino acidsProtein functionCode expansionNon-canonical amino acidsGenetic code expansion techniqueOrthogonal translation systemSkeletal muscle regenerationSelenoprotein functionCell maintenanceBiosynthesis mechanismGenetic systemSelenocysteine insertionPreferred hostMultiple proteinsBiological processesBiology applicationsProtein positionsStop codonCodon sequenceProtein sitesSelenoproteinsChemical biology applicationsMuscle regeneration
2022
Harnessing selenocysteine to enhance microbial cell factories for hydrogen production
Patel A, Mulder D, Söll D, Krahn N. Harnessing selenocysteine to enhance microbial cell factories for hydrogen production. Frontiers In Catalysis 2022, 2: 1089176. PMID: 36844461, PMCID: PMC9961374, DOI: 10.3389/fctls.2022.1089176.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsAncestral 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 acidsUnconventional genetic code systems in archaea
Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Frontiers In Microbiology 2022, 13: 1007832. PMID: 36160229, PMCID: PMC9499178, DOI: 10.3389/fmicb.2022.1007832.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenetic code systemAmino acidsTRNA-dependent pathwayCanonical amino acidsRare amino acidArchaeal lineagesArchaeal speciesSingle lineageArchaeaMolecular mechanismsThird domainExtreme environmentsRecent discoveryLineagesBiochemical elementsHarsh conditionsEukaryotesPyrrolysineSelenocysteineOrganismsSpeciesBacteriaPathwayAcidDiscoveryDiversification 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 moleculesUncovering translation roadblocks during the development of a synthetic tRNA
Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Research 2022, 50: 10201-10211. PMID: 35882385, PMCID: PMC9561287, DOI: 10.1093/nar/gkac576.Peer-Reviewed Original ResearchConceptsOrthogonal translation systemGenetic code expansionCode expansionTertiary interactionsNon-canonical amino acidsAminoacyl-tRNA substratesDomains of lifeAminoacyl-tRNA synthetaseTranslation systemSingle nucleotide mutationsSingle-molecule fluorescenceDistinct tRNAsNon-canonical structuresSelenocysteine insertionRibosomal translationTRNARibosomesSynthetic tRNANucleotide mutationsAmino acidsSame organismP siteOrganismsTranslocationTranslationThe 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 ResearchConceptsFour-base codonsGenetic codeTRNA mutationsAminoacyl-tRNA synthetasesQuadruplet codonsSingle amino acidCodon translationTriplet codonsTRNA synthetasesSynthetic biologistsCodonTRNAAmino acidsChemical alphabetsMutationsMass spectrometrySynthetasesAnticodonToleranceSynthetic systemsBiologistsTranslationEscherichiaNascentDirected Evolution of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Generates a Hyperactive and Highly Selective Variant
Fischer JT, Söll D, Tharp JM. Directed Evolution of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Generates a Hyperactive and Highly Selective Variant. Frontiers In Molecular Biosciences 2022, 9: 850613. PMID: 35372501, PMCID: PMC8965510, DOI: 10.3389/fmolb.2022.850613.Peer-Reviewed Original ResearchKhorana, 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