2025
Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides
Hainzl T, Scortti M, Lindgren C, Grundström C, Krypotou E, Vázquez-Boland J, Sauer-Eriksson A. Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides. Cell Reports 2025, 44: 115290. PMID: 39970044, DOI: 10.1016/j.celrep.2025.115290.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBinding SitesCrystallography, X-RayGlutathioneListeria monocytogenesModels, MolecularOligopeptidesPeptide Termination FactorsProtein BindingVirulenceConceptsDNA-binding helix-turn-helix motifInhibit virulence gene expressionVirulence gene expressionPathogen Listeria monocytogenesPrfA activityVirulence factorsPrfAMaster regulatorsHydrophobic residuesInhibitory bindingGene expressionStructural basisBinding promiscuityPeptide bindingBinding sitesConformational changesPeptide residuesOligopeptidesPeptideInhibitory peptidesBindingPeptide backboneResiduesPromiscuous inhibitionExpressionEngineering 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 ResearchMeSH KeywordsCodon, TerminatorEscherichia coliEscherichia coli ProteinsGenetic CodeGenetic EngineeringGenome, BacterialPeptide Termination FactorsProtein Biosynthesis
2015
Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation
Malinovska L, Palm S, Gibson K, Verbavatz J, Alberti S. Dictyostelium discoideum has a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e2620-e2629. PMID: 25941378, PMCID: PMC4443358, DOI: 10.1073/pnas.1504459112.Peer-Reviewed Original ResearchMeSH KeywordsDictyosteliumElectrophoresis, Polyacrylamide GelFluorescence Recovery After PhotobleachingHumansHuntingtin ProteinMicroscopy, ElectronMicroscopy, FluorescenceNerve Tissue ProteinsPeptide Termination FactorsPrionsProtein Aggregation, PathologicalProteomeProteostasis DeficienciesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsPrion-like proteinsD. discoideumMolecular chaperonesDictyostelium discoideumHuntingtin exon 1Yeast prion protein Sup35Prion-like domainsOverall aggregation propensityProtein-misfolding diseasesUbiquitin-proteasome systemPrion protein Sup35Rich proteomeHsp100 familyCellular proteostasisPrion stateCytosolic aggregatesSequence similarityPrion domainBioinformatics toolsProtein aggregationProteostatic capacityDiscoideumAggregation propensityProteomePrion protein
2014
Revealing the amino acid composition of proteins within an expanded genetic code
Aerni HR, Shifman MA, Rogulina S, O'Donoghue P, Rinehart J. Revealing the amino acid composition of proteins within an expanded genetic code. Nucleic Acids Research 2014, 43: e8-e8. PMID: 25378305, PMCID: PMC4333366, DOI: 10.1093/nar/gku1087.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsCodon, TerminatorEscherichia coliEscherichia coli ProteinsGene DeletionPeptide Termination FactorsPhosphoserineProtein BiosynthesisProteinsProteomicsConceptsNon-standard amino acidsOrthogonal translation systemGenetic codeUAG codonProtein synthesisConventional proteomic analysisRecombinant reporter proteinRelease factor 1Amino acid insertionAmino acid compositionReporter proteinProteomic analysisExtended proteinSurprising diversityUAG readthroughAcid insertionProteomic workflowStop codonNative proteinCodonEscherichia coliAmino acidsMessenger RNAUAGProtein
2013
Genomically Recoded Organisms Expand Biological Functions
Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically Recoded Organisms Expand Biological Functions. Science 2013, 342: 357-360. PMID: 24136966, PMCID: PMC4924538, DOI: 10.1126/science.1241459.Peer-Reviewed Original ResearchConceptsNew genetic codesRelease factor 1UAG stop codonNonstandard amino acidsEscherichia coli MG1655UAA codonGenetic codeColi MG1655Biological functionsStop codonChemical diversityT7 bacteriophageAmino acidsFactor 1CodonMG1655OrganismsProteinDiversityDeletionBacteriophagesViral resistanceTranslation functionGROVivo
2012
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion
Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L, Olds W, Fischer JT, Söll D, Isaacs FJ, Rinehart J. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Letters 2012, 586: 3716-3722. PMID: 22982858, PMCID: PMC3473164, DOI: 10.1016/j.febslet.2012.08.031.Peer-Reviewed Original ResearchConceptsUAG codonEscherichia coli protein synthesisRelease factor 1Aminoacyl-tRNA synthetaseCellular fitnessCodon reassignmentEssential genesElongation factorPhosphoserine phosphataseProtein synthesisRF-1Protein yieldTranslation systemFactor 1CodonAccompanying lossGFPUAAGenesSynthetaseDeletionWNK4FitnessPhosphataseExpression
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