2025
Spermidine is a key polyamine required by intracellular parasites for survival within host erythrocytes
Singh P, Choi J, Cornillot E, Mamoun C. Spermidine is a key polyamine required by intracellular parasites for survival within host erythrocytes. Science Advances 2025, 11: eadv2397. PMID: 40531988, PMCID: PMC12175890, DOI: 10.1126/sciadv.adv2397.Peer-Reviewed Original ResearchConceptsSpermidine biosynthesisIntracellular parasitesRegulate protein translationOxidative stress defenseDe novo synthesisProduction of reactive oxygen speciesTranslational regulationIncreased production of reactive oxygen speciesMolecular functionsProtein translationStress defensePlasmodium falciparum</i>Evolutionary adaptationReactive oxygen speciesAgent of human babesiosisIntraerythrocytic developmentBiosynthesisOxygen speciesHost erythrocytesTherapeutic targetOrchestrating Neural Development Through mRNA Translation Regulation
Rodrigue B, Sajish M, Salmaso N, Aguilar‐Valles A. Orchestrating Neural Development Through mRNA Translation Regulation. Journal Of Neurochemistry 2025, 169: e70128. PMID: 40509688, PMCID: PMC12163303, DOI: 10.1111/jnc.70128.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainGene Expression Regulation, DevelopmentalHumansNeurogenesisProtein BiosynthesisRNA, MessengerConceptsMRNA translation regulationRegulation of mRNA translationMammalian/mechanistic target of rapamycin complex 1MRNA translationTranslational regulationFragile X Messenger Ribonucleoprotein 1Neural developmentGene expressionRegulation of gene expressionCell fate decisionsControlling gene expressionControl of brain developmentTarget of rapamycin complex 1Integrated stress responseNeuronal growth conesDysregulation of mRNA translationRapamycin complex 1Fate decisionsSubcellular compartmentsTranscriptional controlSignaling cascadesFragile X syndromeAxon guidanceMammalian/mechanistic targetStem cell proliferationNeuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators
Malone T, Wu J, Zhang Y, Licznerski P, Chen R, Nahiyan S, Pedram M, Jonas E, Kaczmarek L. Neuronal potassium channel activity triggers initiation of mRNA translation through binding of translation regulators. Science Advances 2025, 11: eadv3140. PMID: 40435242, PMCID: PMC12118559, DOI: 10.1126/sciadv.adv3140.Peer-Reviewed Original ResearchConceptsMRNA translationTranslational regulationInitiation of mRNA translationInitiation of translationSevere intellectual disabilityRegulation of translationMRNA translation regulationNeurites of cortical neuronsB-actinChannel activityIntellectual disabilityPotassium channel activityNeuronal activityMolecular mechanismsInhibit initiationMutationsCell linesPharmacological stimulationCortical neuronsMRNABindingRegulationTranslationEIF4ECYFIP1Cell-Free Protein Synthesis as a Method to Rapidly Screen Machine Learning-Generated Protease Variants
Thornton E, Boyle J, Laohakunakorn N, Regan L. Cell-Free Protein Synthesis as a Method to Rapidly Screen Machine Learning-Generated Protease Variants. ACS Synthetic Biology 2025, 14: 1710-1718. PMID: 40304425, PMCID: PMC12090339, DOI: 10.1021/acssynbio.5c00062.Peer-Reviewed Original ResearchMeSH KeywordsCell-Free SystemKineticsMachine LearningPeptide HydrolasesProtein BiosynthesisProtein EngineeringEukaryotic Microproteins
Jaunbocus N, Ebenki V, Su H, Slavoff S. Eukaryotic Microproteins. Annual Review Of Biochemistry 2025, 94: 1-28. PMID: 40245354, PMCID: PMC12207985, DOI: 10.1146/annurev-biochem-080124-012840.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHumansMicropeptidesOpen Reading FramesPeptidesProtein BiosynthesisRibosomesSaccharomyces cerevisiaeGuidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Loughran G, Andreev D, Terenin I, Namy O, Mikl M, Yordanova M, McManus C, Firth A, Atkins J, Fraser C, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel S, Mankin A, Mariotti M, Tanenbaum M, Topisirovic I, Vázquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark P, Dinman J, Farabaugh P, Gilbert W, Ivanov P, Kieft J, Mühlemann O, Sachs M, Shatsky I, Sonenberg N, Steckelberg A, Willis A, Woodside M, Valasek L, Dmitriev S, Baranov P. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature Structural & Molecular Biology 2025, 32: 418-430. PMID: 40033152, DOI: 10.1038/s41594-025-01492-x.Peer-Reviewed Original ResearchMeSH KeywordsEukaryotaGenes, ReporterGuidelines as TopicHumansProtein BiosynthesisResearch DesignRNA, MessengerConceptsInternal ribosome entry siteGene expression reportersStop codon readthroughRibosome entry siteEukaryotic translationTranscription initiationAntisense transcriptsRegulatory elementsRibosomal frameshiftingCodon readthroughExpression reportersEntry siteDual reportersUnconventional mechanismSequencePolyadenylationMisinterpretation of dataExpressionReadthroughFrameshiftSplicingTranscriptionEvaluate published dataMinimal requirementsProteinEngineering 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
NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development
Strayer E, Krishna S, Lee H, Vejnar C, Neuenkirchen N, Gupta A, Beaudoin J, Giraldez A. NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development. Nature Communications 2024, 15: 10898. PMID: 39738051, PMCID: PMC11685710, DOI: 10.1038/s41467-024-55274-y.Peer-Reviewed Original ResearchConceptsMassively parallel reporter assaysCis-regulatory elementsMaternal-to-zygotic transitionGC-rich motifsU-rich motifsTrans-acting proteinsRepressor of translationRibosome affinity purificationRegulatory grammarUpstream ORFsZygotic expressionTranslational switchReporter mRNATranslational controlTranslational regulationNascent peptideAffinity purificationMicroRNA sitesPolysome profilingMRNA translationZebrafish developmentMRNA stabilityExpression of miR-430MiR-430Regulatory functionsQuantitative profiling of human translation initiation reveals elements that potently regulate endogenous and therapeutically modified mRNAs
Lewis C, Xie L, Bhandarkar S, Jin D, Abdallah K, Draycott A, Chen Y, Thoreen C, Gilbert W. Quantitative profiling of human translation initiation reveals elements that potently regulate endogenous and therapeutically modified mRNAs. Molecular Cell 2024, 85: 445-459.e5. PMID: 39706187, PMCID: PMC11780321, DOI: 10.1016/j.molcel.2024.11.030.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsHEK293 CellsHumansmRNA VaccinesPeptide Chain Initiation, TranslationalProtein BiosynthesisPseudouridineRibosomesRNA, MessengerConceptsTranslation initiationUntranslated regionHuman 5'-untranslated regionChemically modified nucleotidesHigh-throughput methodRibosome recruitmentAlternative isoformsRegulatory elementsEnhanced translationDissecting mechanismsTherapeutic mRNANucleotideTherapeutic proteinsMRNADelivery of therapeutic proteinsSequenceMRNA vaccinesEndogenous RNAQuantitative profilingWidespread effectsTranslation outputRNATherapeuticsIsoformsCellular immunogenicityCotranslational molecular condensation of cochaperones and assembly factors facilitates axonemal dynein biogenesis
Li Y, Xu W, Cheng Y, Djenoune L, Zhuang C, Cox A, Britto C, Yuan S, Wang S, Sun Z. Cotranslational molecular condensation of cochaperones and assembly factors facilitates axonemal dynein biogenesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2402818121. PMID: 39541357, PMCID: PMC11588059, DOI: 10.1073/pnas.2402818121.Peer-Reviewed Original ResearchMeSH KeywordsAxonemal DyneinsAxonemeChlamydomonas reinhardtiiMolecular ChaperonesProtein BiosynthesisRNA, MessengerConceptsDynein axonemal assembly factorsAssembly factorsCytosolic fociOuter dynein armsMacromolecular machinesAxonemal dyneinsAssembly hubDynein armsMolecular condensateLiquid-liquid phase separationCochaperoneEncoding mRNAFoci formationCiliary motilityStable interactionLRRC6Functional significanceRUVBL1DyneinMRNAAssembly of multiple componentsAssemblyPotential mechanismsRUVBL2BiogenesisApplications of cell free protein synthesis in protein design
Thornton E, Paterson S, Stam M, Wood C, Laohakunakorn N, Regan L. Applications of cell free protein synthesis in protein design. Protein Science 2024, 33: e5148. PMID: 39180484, PMCID: PMC11344276, DOI: 10.1002/pro.5148.Peer-Reviewed Original ResearchUPF1 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 analysisUTRRecent developments, opportunities, and challenges in the study of mRNA pseudouridylation
Gilbert W. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA 2024, 30: rna.079975.124. PMID: 38531650, PMCID: PMC11019745, DOI: 10.1261/rna.079975.124.Peer-Reviewed Original Research
2023
Mapping RNA translation
Fan R. Mapping RNA translation. Science 2023, 380: 1321-1322. PMID: 37384700, DOI: 10.1126/science.adi6844.Peer-Reviewed Original ResearchMistranslation 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 ResearchMeSH KeywordsAmino AcidsCodonEscherichia coliGenetic CodeHumansMutationProlineProtein BiosynthesisProteinsProteomeRNA, TransferStreptomycesThreonineConceptsTransfer 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 conditionsMapping the in vivo fitness landscape of a tethered ribosome
Radford F, Rinehart J, Isaacs F. Mapping the in vivo fitness landscape of a tethered ribosome. Science Advances 2023, 9: eade8934. PMID: 37115918, PMCID: PMC10146877, DOI: 10.1126/sciadv.ade8934.Peer-Reviewed Original ResearchConceptsPeptidyl transfer centerEpistatic interactionsFitness landscapeMacromolecular machinesLaboratory evolutionRibosome functionDeleterious mutationsVivo fitness landscapeComplete mutagenesisLethal mutationsGenetic elementsRibosomesProtein synthesisDominant lethal mutationsMost nucleotidesMutationsSequence spaceNucleotidesNext-generation biomaterialsLandscapeMutagenesisOrganismsSequenceInteractionDeeper understandingCMPK2 restricts Zika virus replication by inhibiting viral translation
Pawlak J, Hsu J, Xia H, Han P, Suh H, Grove T, Morrison J, Shi P, Cresswell P, Laurent-Rolle M. CMPK2 restricts Zika virus replication by inhibiting viral translation. PLOS Pathogens 2023, 19: e1011286. PMID: 37075076, PMCID: PMC10150978, DOI: 10.1371/journal.ppat.1011286.Peer-Reviewed Original ResearchConceptsCytidine/uridine monophosphate kinase 2I interferon-stimulated genesZika virus replicationYellow fever virusAntiviral activityAntiviral effectVirus replicationKunjin virusType I interferon-stimulated genesFirst lineOverall antiviral responseHost's first lineEffective therapeutic interventionsViral translationBroad antiviral activityInterferon-stimulated genesGlobal health threatAntiviral treatmentFlaviviral infectionsPathogenic flavivirusesAntiviral functionDrug AdministrationTherapeutic interventionsAntiviral responseDengue virusSarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism
Lomakin I, Devarkar S, Patel S, Grada A, Bunick C. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Research 2023, 51: 2915-2930. PMID: 36864821, PMCID: PMC10085706, DOI: 10.1093/nar/gkad103.Peer-Reviewed Original ResearchMeSH KeywordsAcne VulgarisAnti-Bacterial AgentsHumansPropionibacterium acnesProtein BiosynthesisRibosomesTetracyclinesSplit 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 ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesCodon, TerminatorEscherichia coliHumansLigasesProtein BiosynthesisRNA, TransferConceptsAminoacyl-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 applications
2022
Cellular Stress-Induced Metabolites in Escherichia coli
Gatsios A, Kim C, York A, Flavell R, Crawford J. Cellular Stress-Induced Metabolites in Escherichia coli. Journal Of Natural Products 2022, 85: 2626-2640. PMID: 36346625, PMCID: PMC9949963, DOI: 10.1021/acs.jnatprod.2c00706.Peer-Reviewed Original ResearchMeSH KeywordsErythromycinEscherichia coliHumansNaphthoquinonesProtein BiosynthesisStress, PhysiologicalTryptophanTryptophan-tRNA Ligase
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply