2025
Super‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT
Bhaskar H, Gidden Z, Virdi G, Kleinjan D, Rosser S, Gandhi S, Regan L, Horrocks M. Super‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT. Protein Science 2025, 34: e70008. PMID: 39865341, PMCID: PMC11761688, DOI: 10.1002/pro.70008.Peer-Reviewed Original Research
2024
Microbial metabolism of host-derived antioxidants
Zhou Z, Hatzios S. Microbial metabolism of host-derived antioxidants. Current Opinion In Chemical Biology 2024, 84: 102565. PMID: 39721219, PMCID: PMC11863140, DOI: 10.1016/j.cbpa.2024.102565.Peer-Reviewed Original ResearchEfficient Genome Editing Using ‘NanoMEDIC’ AsCas12a-VLPs Produced with Pol II-Transcribed crRNA
Borovikova S, Shepelev M, Mazurov D, Kruglova N. Efficient Genome Editing Using ‘NanoMEDIC’ AsCas12a-VLPs Produced with Pol II-Transcribed crRNA. International Journal Of Molecular Sciences 2024, 25: 12768. PMID: 39684477, PMCID: PMC11641575, DOI: 10.3390/ijms252312768.Peer-Reviewed Original ResearchRNA ribonucleoprotein complexVirus-like particlesGenome editingProcesses pre-crRNARNA polymerase IIIEfficient genome editingTargeted genome editingJurkat T cellsGene therapy applicationsMature crRNAsPre-crRNAPolymerase IIICas nucleasesRibonucleoprotein complexEfficient targeted genome editingCrRNAMammalian cellsLevels of gene editingPackaging mechanismPromoter usageU6 promoterT cellsEditing efficiencyCXCR4 knockoutGene editingA Divergent Synthesis of Numerous Pyrroloiminoquinone Alkaloids Identifies Promising Antiprotozoal Agents
Barnes G, Magann N, Perrotta D, Hörmann F, Fernandez S, Vydyam P, Choi J, Prudhomme J, Neal A, Le Roch K, Mamoun C, Vanderwal C. A Divergent Synthesis of Numerous Pyrroloiminoquinone Alkaloids Identifies Promising Antiprotozoal Agents. Journal Of The American Chemical Society 2024, 146: 29883-29894. PMID: 39412402, PMCID: PMC11528414, DOI: 10.1021/jacs.4c11897.Peer-Reviewed Original ResearchNatural productsLarock indole synthesisAlkaloid natural productsAmine nucleophilesDivergent synthesisIndole synthesisPyrrolic nitrogenMethoxy groupLead compoundsDrug discoveryCompoundsStructural analogsPlasmodium falciparum</i>SynthesisPyrroloiminoquinoneHuman cytotoxicityMalaria parasitesNucleophilesPyrroleAntiprotozoal agentsAminesMammalian cellsIntermediateEffective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs
Marquart K, Mathis N, Mollaysa A, Müller S, Kissling L, Rothgangl T, Schmidheini L, Kulcsár P, Allam A, Kaufmann M, Matsushita M, Haenggi T, Cathomen T, Kopf M, Krauthammer M, Schwank G. Effective genome editing with an enhanced ISDra2 TnpB system and deep learning-predicted ωRNAs. Nature Methods 2024, 21: 2084-2093. PMID: 39313558, DOI: 10.1038/s41592-024-02418-z.Peer-Reviewed Original ResearchThe physiological and pathological roles of RNA modifications in T cells
Deng Y, Zhou J, Li H. The physiological and pathological roles of RNA modifications in T cells. Cell Chemical Biology 2024, 31: 1578-1592. PMID: 38986618, DOI: 10.1016/j.chembiol.2024.06.003.Peer-Reviewed Original ResearchRNA modificationsDynamic chemical modificationsInternal RNA modificationFunctions of mammalian cellsT cell developmentPathological roleRNA transcriptsCellular stimuliMammalian cellsRNA moleculesPost-transcriptionallyT cell biologyT cell survivalT cellsCell developmentCell survivalCell biologyRNAT cell-based immunotherapyCell-based immunotherapyT cell immunityAdaptive immunityCellsDifferentiationCell immunityDifferential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage
Rodríguez J, Uche O, Gao S, Lee S, Airola M, Bahmanyar S. Differential reliance of CTD-nuclear envelope phosphatase 1 on its regulatory subunit in ER lipid synthesis and storage. Molecular Biology Of The Cell 2024, 35: ar101. PMID: 38776127, PMCID: PMC11244170, DOI: 10.1091/mbc.e23-09-0382.Peer-Reviewed Original ResearchLipin-1Lipid synthesisPhosphatase 1Lipid storageLipid dropletsLipid droplet biogenesisER enzymeER sizeER expansionCellular demandAmphipathic helixSynthesis of glycerophospholipidsProteasomal degradationRegulatory subunitMammalian cellsMembrane expansionN-terminusBinding interfaceLipid intermediatesNuclear envelopeMembrane synthesisLipidMetabolic conditionsBiogenesisLipinStructure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology
Gao S, Rodríguez J, Bahmanyar S, Airola M. Structure and mechanism of the human CTDNEP1–NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2321167121. PMID: 38776370, PMCID: PMC11145253, DOI: 10.1073/pnas.2321167121.Peer-Reviewed Original ResearchConceptsProtein phosphatase complexPhosphatase complexER membrane biogenesisHigh-resolution crystal structuresProtein serine/threonine phosphatasesCancer-associated mutationsDevelopment of medulloblastomaMembrane biogenesisSubstrate recognitionER expansionActive siteRegulatory subunitSubstrate peptideMammalian cellsSerine/threonine phosphataseIdentical phenotypesArg residuesMolecular detailsSubunit 1Phosphatase 1Inactivating mutationsPeptide sequencesAggressive childhood cancerMutationsPhosphatase activityCOPII with ALG2 and ESCRTs control lysosome-dependent microautophagy of ER exit sites
Liao Y, Pang S, Li W, Shtengel G, Choi H, Schaefer K, Xu C, Lippincott-Schwartz J. COPII with ALG2 and ESCRTs control lysosome-dependent microautophagy of ER exit sites. Developmental Cell 2024, 59: 1410-1424.e4. PMID: 38593803, DOI: 10.1016/j.devcel.2024.03.027.Peer-Reviewed Original ResearchEndoplasmic reticulum exit sitesER exit sitesAmino acid starvationPurified recombinant componentsExit siteProtein sortingSecretory pathwayMammalian cellsNutrient stressCellular conditionsEndoplasmic reticulumGiant unilamellar vesiclesTubular outgrowthsESCRTMicroautophagyNutrient stressorsALG2COPIILysosomesPathwayMTOR inhibitionUnilamellar vesiclesRecombinant componentsFocused ion beam scanning electron microscopyIon beam scanning electron microscopyProtein oxidation of fucose environments (POFE) reveals fucose–protein interactions
Xie Y, Chen S, Alvarez M, Sheng Y, Li Q, Maverakis E, Lebrilla C. Protein oxidation of fucose environments (POFE) reveals fucose–protein interactions. Chemical Science 2024, 15: 5256-5267. PMID: 38577366, PMCID: PMC10988611, DOI: 10.1039/d3sc06432h.Peer-Reviewed Original ResearchProtein-protein interactionsCopper-catalyzed click chemistryFormation of hydroxyl radicalsCell membrane glycoproteinMembrane glycoproteinPost-translational modificationsLiquid chromatography coupled with tandem mass spectrometryTandem mass spectrometryClick chemistryBinding partnersGalectin-3-binding proteinProtein functionCellular processesMammalian cellsMass spectrometryOxidized peptidesFucose residuesHydroxyl radicalsLabeled probesBioorthogonal groupsLC-MS/MSAmino acidsProteinFucoseProtein oxidationUnraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging
Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman J, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024, 187: 1769-1784.e18. PMID: 38552613, DOI: 10.1016/j.cell.2024.02.033.Peer-Reviewed Original ResearchConceptsInter-organelle contactsSuper-resolutionMultiplexed super-resolution microscopyIntricate spatial relationshipsGolgi stacksMammalian cellsCellular functionsSuper-resolution microscopyPrimary ciliaSuper-resolution fluorescence microscopyCellular complexityTransient adaptationFluorescence microscopyDNA-PAINTFluorogenic labelingMolecular targetsSpatial relationshipsImagesThroughputAdaptive inhibition of CGAS signaling by TREX1
Lira M, Vanpouille-Box C, Galluzzi L. Adaptive inhibition of CGAS signaling by TREX1. Trends In Cancer 2024, 10: 177-179. PMID: 38355355, PMCID: PMC11075008, DOI: 10.1016/j.trecan.2024.02.001.Peer-Reviewed Original ResearchCell surface RNAs control neutrophil recruitment
Zhang N, Tang W, Torres L, Wang X, Ajaj Y, Zhu L, Luan Y, Zhou H, Wang Y, Zhang D, Kurbatov V, Khan S, Kumar P, Hidalgo A, Wu D, Lu J. Cell surface RNAs control neutrophil recruitment. Cell 2024, 187: 846-860.e17. PMID: 38262409, PMCID: PMC10922858, DOI: 10.1016/j.cell.2023.12.033.Peer-Reviewed Original ResearchConceptsCell surfaceMammalian homologOuter cell surfaceRNA transportGlycan modificationsMammalian cellsSID-1Cellular functionsRecruitment to inflammatory sitesGlycoRNARNAMurine neutrophilsFunctional significanceNeutrophil recruitmentNeutrophil recruitment to inflammatory sitesBiological importanceCellsNeutrophil adhesionReduced neutrophil adhesionHomologyGlycansGenesInflammatory sitesRecruitmentEndothelial cells
2023
Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis
Shi X, DeCiucis M, Grabinska K, Kanyo J, Liu A, Lam T, Shen H. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Molecular Cell 2023, 84: 802-810.e6. PMID: 38157846, PMCID: PMC10922821, DOI: 10.1016/j.molcel.2023.12.008.Peer-Reviewed Original ResearchProtein quality controlMitochondrial protein quality controlDual regulationMetabolic compartmentalizationIron homeostasisMitochondrial iron-sulfur clustersIron-sulfur clustersMitochondrial transportersProtein regulationMammalian cellsCRISPR knockoutCysteine residuesTransporter regulationLoop 1SLC25A39Glutathione homeostasisMetabolic sensingGlutathione uptakeMature neuronsProtein levelsHomeostasisRegulationAFG3L2Biochemical featuresMitochondrial glutathione levelsCell Surface RNAs Control Neutrophil Function
Zhang N, Tang W, Torres L, Zhu L, Wang X, Ajaj Y, Wang Y, Zhang D, Kurbatov V, Zhou H, Luan Y, Kumar P, Hidalgo A, Wu D, Lu J. Cell Surface RNAs Control Neutrophil Function. Blood 2023, 142: 674. DOI: 10.1182/blood-2023-187570.Peer-Reviewed Original ResearchExtracellular RNaseCell surfaceTotal RNABona fide ligandsEndothelial cellsOuter cell surfaceTransendothelial migrationMammalian cellsSuch RNAsGlycan modificationsCellular RNAGlycoRNARNase digestionLive cellsRNAHematopoietic cellsRNase treatmentSimilar defectsIntegrin levelsConfocal microscopyRNaseGlycan fractionImportant functionsHomologuesRecombinant E-selectinA dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin
Sahu S, Ekundayo B, Kumar A, Bleichert F. A dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin. The EMBO Journal 2023, 42: embj2023114654. PMID: 37551430, PMCID: PMC10505921, DOI: 10.15252/embj.2023114654.Peer-Reviewed Original ResearchConceptsOrigin recognition complexH4K20 trimethylationHeterochromatin replicationRecognition complexCryo-electron microscopy structureLocal chromatin environmentSpecific histone marksSpecific chromatin contextsMcm2-7 loadingTernary complex assemblyChromatin environmentChromatin marksChromatin contextHistone marksHistone modificationsReplication initiationEukaryotic cellsMicroscopy structureChromatin condensatesORC recruitmentDNA replicationMammalian cellsNucleosomal DNAAromatic cageComplex assemblyIsotope tracing reveals bacterial catabolism of host-derived glutathione during Helicobacter pylori infection
Baskerville M, Kovalyova Y, Mejías-Luque R, Gerhard M, Hatzios S. Isotope tracing reveals bacterial catabolism of host-derived glutathione during Helicobacter pylori infection. PLOS Pathogens 2023, 19: e1011526. PMID: 37494402, PMCID: PMC10406306, DOI: 10.1371/journal.ppat.1011526.Peer-Reviewed Original ResearchConceptsH. pylori infectionPylori infectionInfected cellsBacterial catabolismGastric pathogen Helicobacter pyloriGSH depletionPathogen Helicobacter pyloriH. pylori-infected cellsMammalian cellsReactive oxygen speciesHelicobacter pylori infectionH. pylori colonizationCellular biomoleculesGSH homeostasisBacterial acquisitionCertain bacteriaVirulence factorsAntioxidant glutathioneIntracellular GSHOxidative damageOxidized GSHΓ-glutamyl transpeptidaseIsotope tracingHost tissuesOxygen speciesAlternative glucose uptake mediated by β-catenin/RSK1 axis under stress stimuli in mammalian cells
Wang C, Lin R, Qi X, Xu Q, Sun X, Zhao Y, Jiang T, Jiang J, Sun Y, Deng Y, Wen J. Alternative glucose uptake mediated by β-catenin/RSK1 axis under stress stimuli in mammalian cells. Biochemical Pharmacology 2023, 214: 115645. PMID: 37321415, DOI: 10.1016/j.bcp.2023.115645.Peer-Reviewed Original ResearchConceptsPhosphorylation of TBC1D4Glucose uptakeGlucose transportActivation of RSK1Stress conditionsMechanism of glucose uptakeTranslocation of GLUT4Translocation of glucose transportersGlucose transporter translocationStress stimuliIncreased glucose uptakeB-cateninGlucose starvationEfficiency of glucose uptakeProtein complexesMammalian cellsScaffold proteinStress signalsCellular energy utilizationFamily 4TBC1D4Kinase activityRSK1Cellular adaptationCellular membranesTunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior
Nguyen R, Cabral A, Rossello‐Martinez A, Zulli A, Gong X, Zhang Q, Yan J, Mak M. Tunable Mesoscopic Collagen Island Architectures Modulate Stem Cell Behavior. Advanced Materials 2023, 35: e2207882. PMID: 36895051, PMCID: PMC10166061, DOI: 10.1002/adma.202207882.Peer-Reviewed Original ResearchConceptsStem cell behaviorCell behaviorPluripotent stem cellsMesenchymal stem cell behaviorMammalian cellsMesodermal differentiationCell migrationExtracellular matrixStem cellsOsteogenic differentiationRegional enrichmentCollagen-based hydrogelsPhysiological tissuesBioactive cuesDifferentiationBiophysical environmentCollagen hydrogelsCellsIslandsComplex architectureTissue engineering applicationsTissueCollagen architectureEnrichmentGelSplit 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 applications
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