2025
Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor.
Nicholson-Shaw T, Dowdle M, Ajaj Y, Perelis M, Fulzele A, Yeo G, Bennett E, Lykke-Andersen J. Human CCR4 deadenylase homolog Angel1 is a Non-Stop mRNA Decay factor. RNA 2025, rna.080399.125. PMID: 40441874, DOI: 10.1261/rna.080399.125.Peer-Reviewed Original ResearchMRNA decayRibosome-associated quality controlAbsence of stop codonsQuality control pathwaysMRNA decay factorsMRNA coding regionNonsense-mediated decayTargets aberrant mRNAsNascent polypeptidesCatalytic residuesPremature polyadenylationReporter mRNAAberrant mRNAsCoding regionStabilization of reporter mRNAsStop codonAngel1Control pathwaysBiochemical activityHuman cellsCodonMRNAPathwayDecayPolyadenylationEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original Research
2024
UPF1 regulates mRNA stability by sensing poorly translated coding sequences
Musaev D, Abdelmessih M, Vejnar C, Yartseva V, Weiss L, Strayer E, Takacs C, Giraldez A. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Reports 2024, 43: 114074. PMID: 38625794, PMCID: PMC11259039, DOI: 10.1016/j.celrep.2024.114074.Peer-Reviewed Original ResearchConceptsUpstream open reading framesOpen reading frameRegulate mRNA stabilityNonsense-mediated decayMRNA stabilityReading frameOpen reading frame lengthRegulate mRNA decayAU-rich elementsMicroRNA binding sitesCis-elementsTranslation initiationStop codonMRNA decayCodon optimizationUPF1Gene expressionBinding sitesCodonMRNAConvergent rolesHigher decay ratesMachine-learning analysisUTRNon-mutational neoantigens in disease
Stern L, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nature Immunology 2024, 25: 29-40. PMID: 38168954, PMCID: PMC11075006, DOI: 10.1038/s41590-023-01664-1.Peer-Reviewed Original ResearchConceptsNon-canonical initiation codonsPost-translational protein modificationMature T cellsRibosomal RNA processingAlternative RNA splicingProtein-coding regionsNon-mutational mechanismsAbility of mammalsRNA processingRNA splicingInitiation codonProtein modificationHuman diseasesMature T cell repertoireAntigenic peptidesImmune recognitionAdaptive immune responsesT cellsAntigenic determinantsMHC class ICellsSplicingNovel antigenic determinantsMammalsCodon
2023
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression
Narunsky A, Kavita K, Panchapakesan S, Fris M, Breaker R. A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression. Microbial Genomics 2023, 9: mgen001019. PMID: 37233150, PMCID: PMC10272879, DOI: 10.1099/mgen.0.001019.Peer-Reviewed Original ResearchConceptsBranched-chain amino acidsRNA motifsUpstream open reading framesTranscription attenuation mechanismStructured noncoding RNAsOpen reading frameRiboswitch classesTranscription attenuationProtein translationNoncoding RNAsOperon expressionGenetic approachesReading frameStart codonUORF translationStop codonBacterial speciesHost cellsGenesUORFsAmino acidsMotifCodonCommon mechanismCorynebacterium species
2022
Therapeutic Targeting of RAS Mutant Cancers
Stites E, Paskvan K, Kato S. Therapeutic Targeting of RAS Mutant Cancers. 2022 DOI: 10.1017/9781009064828.Peer-Reviewed Original ResearchMeasuring 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 systemsBiologistsTranslationEscherichiaNascentIr56b is an atypical ionotropic receptor that underlies appetitive salt response in Drosophila
Dweck HKM, Talross GJS, Luo Y, Ebrahim SAM, Carlson JR. Ir56b is an atypical ionotropic receptor that underlies appetitive salt response in Drosophila. Current Biology 2022, 32: 1776-1787.e4. PMID: 35294865, PMCID: PMC9050924, DOI: 10.1016/j.cub.2022.02.063.Peer-Reviewed Original ResearchConceptsSalt tasteBitter-sensing neuronsStop codonLoss of functionNumber of speciesIonotropic receptorsIonotropic receptor familyN-terminal regionReceptor familyNeuronsDrosophila speciesPremature stop codonTaste modalitiesAncient functionGR familySalt responseSense codonsMolecular basisAtypical memberSalt detectionModalitiesCodonSensory modalitiesDrosophilaBehavioral responsesThe expression of essential selenoproteins during development requires SECIS-binding protein 2–like
Kiledjian N, Shah R, Vetick M, Copeland P. The expression of essential selenoproteins during development requires SECIS-binding protein 2–like. Life Science Alliance 2022, 5: e202101291. PMID: 35210313, PMCID: PMC8881744, DOI: 10.26508/lsa.202101291.Peer-Reviewed Original ResearchConceptsSECIS-binding protein 2Sec insertion sequenceSelenoprotein synthesisProtein 2Amino acid selenocysteineFrame UGA codonDays post fertilizationEssential selenoproteinsCRISPR mutationsSec incorporationUGA codonSelenoprotein mRNAsPost fertilizationRNA structureSe labelingSelenoproteinsFull complementInsertion sequenceEmbryosCodonGenesSBP2Oxidative stressDietary requirementsRelative roles
2021
Tissue-specific dynamic codon redefinition in Drosophila
Hudson AM, Szabo NL, Loughran G, Wills NM, Atkins JF, Cooley L. Tissue-specific dynamic codon redefinition in Drosophila. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2012793118. PMID: 33500350, PMCID: PMC7865143, DOI: 10.1073/pnas.2012793118.Peer-Reviewed Original ResearchConceptsStop codonTranslational stop codon readthroughReadthrough efficiencyHuman tissue culture cellsStop codon readthroughTissue-specific regulationAdult central nervous system (CNS) tissueTissue culture cellsReadthrough productKelch proteinUbiquitin ligaseSingle geneAdult brainIndividual proteinsCodon readthroughReadthroughViral mRNAsC-terminalMalpighian tubulesCodonNeuronal proteinsCell typesAmino acidsCulture cellsDrosophila
2020
Non-AUG start codons: Expanding and regulating the small and alternative ORFeome
Cao X, Slavoff SA. Non-AUG start codons: Expanding and regulating the small and alternative ORFeome. Experimental Cell Research 2020, 391: 111973. PMID: 32209305, PMCID: PMC7256928, DOI: 10.1016/j.yexcr.2020.111973.Peer-Reviewed Original ResearchConceptsSmall open reading framesFunctional small open reading framesStart codonClasses of genesImportant biological processesNon-AUG start codonsOpen reading frameNon-AUG codonsStart codon usageAUG start codonEukaryotic genomesGenomic toolsRibosome profilingNovel genesCodon usageReading frameProteomic studiesBiological processesSequence propertiesCodonGenesPresence of thousandsEukaryotesProkaryotesThe mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation
Han N, Bullwinkle T, Loeb K, Faull K, Mohler K, Rinehart J, Ibba M. The mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. Journal Of Biological Chemistry 2020, 295: 1402-1410. DOI: 10.1016/s0021-9258(17)49898-x.Peer-Reviewed Original ResearchAmino acid activationSerine codonsProtein synthesisHuman protein extractsHuman seryl-tRNA synthetaseAminoacyl-tRNA synthetaseSeryl-tRNA synthetaseAmyotrophic lateral sclerosisAlanyl-tRNA synthetaseN-methylaminoNonproteinogenic amino acidsCotranslational incorporationTRNA aminoacylationAlzheimer's diseaseProtein extractsBiochemical assaysAmino acidsExchange assayBMAAAcid activationSynthetaseCodonAminoacylationNeurodegenerative diseasesMultiple different mechanisms
2019
To Code or Not to Code: What Is the Linc?
Flavell R. To Code or Not to Code: What Is the Linc? The FASEB Journal 2019, 33: 218.1-218.1. DOI: 10.1096/fasebj.2019.33.1_supplement.218.1.Peer-Reviewed Original ResearchNon-canonical proteinsNon-protein codingNon-coding RNAsUnbiased transcriptomics approachMammalian proteinsNovel ORFsRibosome associationUndiscovered proteinsTranscriptomic approachMethionine codonDistinct proteinsFunctional proteinsImportant transcriptsORFProteinEssential roleGenomeAbsolute requirementFASEB JournalGenesRNABacterial infectionsProteinaceous productsMisannotationsCodon
2018
The translation of non-canonical open reading frames controls mucosal immunity
Jackson R, Kroehling L, Khitun A, Bailis W, Jarret A, York AG, Khan OM, Brewer JR, Skadow MH, Duizer C, Harman CCD, Chang L, Bielecki P, Solis AG, Steach HR, Slavoff S, Flavell RA. The translation of non-canonical open reading frames controls mucosal immunity. Nature 2018, 564: 434-438. PMID: 30542152, PMCID: PMC6939389, DOI: 10.1038/s41586-018-0794-7.Peer-Reviewed Original ResearchConceptsNon-canonical open reading framesOpen reading frameProtein-coding genomeReading frameNew open reading framesProtein-coding genesNon-protein codingNon-coding RNAsUnbiased transcriptomics approachTranscriptomic approachMethionine codonDistinct proteinsFunctional proteinsImportant transcriptsEssential roleGenomeAbsolute requirementGenesRNABacterial infectionsProteinaceous productsProteinTranslationMisannotationsCodonSimultaneous zygotic inactivation of multiple genes in mouse through CRISPR/Cas9-mediated base editing
Zhang H, Pan H, Zhou C, Wei Y, Ying W, Li S, Wang G, Li C, Ren Y, Li G, Ding X, Sun Y, Li G, Song L, Li Y, Yang H, Liu Z. Simultaneous zygotic inactivation of multiple genes in mouse through CRISPR/Cas9-mediated base editing. Development 2018, 145: dev168906. PMID: 30275281, DOI: 10.1242/dev.168906.Peer-Reviewed Original ResearchConceptsGene functionMultiple genesHair cell generationProtein-coding sequencesMulti-gene interactionsModel organismsFunctional genesZygotic mutationsGene crucialHigh-throughput screeningBase editingMouse mutantsStop codonSingle mutationGenesCRISPRCell generationGenetic mutationsMutationsMouse breedingNormal hearing functionDrosophilaMutantsBreedingCodonLso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast. PLOS Biology 2018, 16: e2005903. PMID: 30208026, PMCID: PMC6135351, DOI: 10.1371/journal.pbio.2005903.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCodon, InitiatorConserved SequenceGene Expression Regulation, FungalHeLa CellsHumansPeptide Chain Elongation, TranslationalPeptide Chain Termination, TranslationalProtein BiosynthesisRibosomal ProteinsRibosomesRNA, RibosomalRNA, TransferSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsRibosome-binding proteinsRibosome-associated proteinsCodon-specific changesCoiled-coil domainQuantitative mass spectrometryGTPase activation centerRibosome-binding activityMost tRNAsRibosome profilingGene regulationMost genesCellular homeostasisTranslation defectsRibosomal RNATranslational recoveryComplete complementStart codonStop codonLso2Protein synthesisOpen reading frame 2ProteinImportant functionsCodonYeastElongation factor P controls translation of the mgtA gene encoding a Mg2+ transporter during Salmonella infection
Choi E, Nam D, Choi J, Park S, Lee J, Lee E. Elongation factor P controls translation of the mgtA gene encoding a Mg2+ transporter during Salmonella infection. MicrobiologyOpen 2018, 8: e00680. PMID: 29949242, PMCID: PMC6460261, DOI: 10.1002/mbo3.680.Peer-Reviewed Original ResearchConceptsMgtA geneProline codonsControl translationIntramacrophage survivalPathogen Salmonella enterica serovar TyphimuriumElongation factor PConsecutive proline codonsOpen reading frameSalmonella enterica serovar TyphimuriumEnterica serovar TyphimuriumTranslational controlReading frameSalmonella pathogenesisMRNA sequencesGenesCodonSerovar TyphimuriumRibosomesFactor P
2017
The N‐terminus of SECIS Binding Protein 2 is Required for Processive Selenocystine Incorporation in Selenoprotein P
Pinkerton M, Vetick M, Shetty S, Copeland P. The N‐terminus of SECIS Binding Protein 2 is Required for Processive Selenocystine Incorporation in Selenoprotein P. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.600.9.Peer-Reviewed Original ResearchSelenocysteine insertion sequenceN-terminusSec codonAmino acid selenocysteineTranslation elongation factorProtein 2UGA stop codonFull-length proteinIncorporation of SecFrame UGA codonBinding protein 2Sec residueTrans factorsElongation factorMammalian systemsSec incorporationUGA codonC-terminusLength proteinSelenocysteine tRNAUntranslated regionSpecialized functionsStop codonC-terminalCodon
2016
Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation
Alexandrov A, Shu MD, Steitz JA. Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation. Molecular Cell 2016, 65: 191-201. PMID: 28017590, PMCID: PMC5301997, DOI: 10.1016/j.molcel.2016.11.032.Peer-Reviewed Original ResearchConceptsNonsense-mediated decayPremature termination codonNMD factorsNMD pathwayMRNA degradationHuman cellsForward genetic screeningGenetic screen identifiesHuman genetic diseasesHuman candidate genesNonsense suppression therapyModel organismsGenetic screeningScreen identifiesTermination codonCandidate genesGenetic discoveriesReporter fluorescenceGenetic diseasesPathwayAdditional key factorsCellsCRISPRCodonHomologyRNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq
Kelsic E, Chung H, Cohen N, Park J, Wang H, Kishony R. RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Systems 2016, 3: 563-571.e6. PMID: 28009265, PMCID: PMC5234859, DOI: 10.1016/j.cels.2016.11.004.Peer-Reviewed Original ResearchCodon choiceMAGE-seqRNA structureEnhanced translation initiationSynonymous codon choiceRNA folding predictionsDisruption of native structureSynthetic biology applicationsRNA structure determinationAmplicon deep sequencingGenes infACodon distributionCodon preferenceOptimal codonsTranslation initiationFold predictionRNA conformationDeep sequencingCodon optimizationCodonGene expressionCodon mutantsNative structureGenesMutants
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