Featured Publications
Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID
Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Molecular Cell 2022, 82: 2900-2911.e7. PMID: 35905735, PMCID: PMC9662605, DOI: 10.1016/j.molcel.2022.06.035.Peer-Reviewed Original ResearchConceptsSubcellular localizationProximity biotinylationSmall open reading framesAlternative proteinsOpen reading frameHigh-throughput technologiesSubnuclear organellesCanonical proteinsRRNA transcriptionSubcellular compartmentsReading frameProteogenomic identificationProtein compositionAmino acidsMicroproteinsProteinBiotinylationLocalizationTurboIDTranscriptionOrganellesMouse modelPolypeptideNucleoliExpressionNascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor
Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nature Chemical Biology 2022, 18: 643-651. PMID: 35393574, PMCID: PMC9423127, DOI: 10.1038/s41589-022-01003-9.Peer-Reviewed Original ResearchConceptsRibosomal subunitDNA damage stressImportant cellular rolesGlobal protein synthesisN-terminal extensionCellular rolesCanonical proteinsHuman cellsProtein synthesisAlternative proteinsCell proliferationChemoproteomicsDamage stressSubunitsProteinAssemblyInhibitorsHypothesis generationMicroproteinsCytoplasmProliferationCellsExportDepletionAlt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24
Cao X, Khitun A, Luo Y, Na Z, Phoodokmai T, Sappakhaw K, Olatunji E, Uttamapinant C, Slavoff SA. Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24. Nature Communications 2021, 12: 508. PMID: 33479206, PMCID: PMC7820019, DOI: 10.1038/s41467-020-20841-6.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAmino Acid SequenceBase SequenceBiological TransportCell MembraneDown-RegulationEndoplasmic ReticulumHEK293 CellsHumansMembrane ProteinsMutationPhosphatidylinositol 3-KinasesPhosphatidylinositol 4,5-DiphosphateProtein BindingProto-Oncogene Proteins c-aktRibosomal ProteinsSignal TransductionTOR Serine-Threonine KinasesConceptsPI3K-AktEndoplasmic reticulumMTOR signalingHuman gene functionAlternative open reading framesOpen reading framePI3K signalingDifferent molecular mechanismsCanonical proteinsGene functionCell sizeReading framePrecursor phosphatidylinositolPlasma membraneTMEM24Upstream regulatorMolecular mechanismsPhosphoserine residuesK signalingPoint mutationsSignalingPhosphatidylinositolProteinReticulumRPL36
2020
A Genetic Code Expansion‐Derived Molecular Beacon for the Detection of Intracellular Amyloid‐β Peptide Generation
Sappakhaw K, Jantarug K, Slavoff S, Israsena N, Uttamapinant C. A Genetic Code Expansion‐Derived Molecular Beacon for the Detection of Intracellular Amyloid‐β Peptide Generation. Angewandte Chemie 2020, 133: 3980-3985. PMID: 38504667, PMCID: PMC10946459, DOI: 10.1002/ange.202010703.Peer-Reviewed Original ResearchDiverse biological functionsAmyloid precursor proteinProteolytic proteoformsEndocytic pathwayGenetic taggingBiological functionsProtein precursorLiving cellsProteolytic processingMolecular beacon designPrecursor proteinCellular studiesLabeling strategyProteoformsMolecular beaconsAmyloid-β peptide generationBiogenesisImportant rolePeptide generationBeacon designPolypeptideReporterProteinAlzheimer's diseasePathway
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 productsProteinTranslationMisannotationsCodonP‑Bodies: Composition, Properties, and Functions
Luo Y, Na Z, Slavoff SA. P‑Bodies: Composition, Properties, and Functions. Biochemistry 2018, 57: 2424-2431. PMID: 29381060, PMCID: PMC6296482, DOI: 10.1021/acs.biochem.7b01162.Peer-Reviewed Original ResearchConceptsP-bodiesMRNA decayMRNA decay machineryLiquid-liquid phase separationP-body functionPost-transcriptional regulationDecay machineryProcessing bodiesTranslational repressionEukaryotic cellsCytoplasmic ribonucleoproteinCellular localizationRibonucleoproteinMolecular compositionRecent advancesRepressionMachineryProteinMRNARegulationFunctionCellsLocalizationDiscoveryComposition
2017
Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli
D’Lima N, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli. Journal Of Proteome Research 2017, 16: 3722-3731. PMID: 28861998, PMCID: PMC5647875, DOI: 10.1021/acs.jproteome.7b00419.Peer-Reviewed Original ResearchConceptsCold shock proteinsComparative proteomicsShock proteinsRelated Gram-negative bacteriaMass spectrometry-based proteomicsSmall open reading framesMolecular genetic approachesWhole genome databaseSpectrometry-based proteomicsOpen reading frameE. coliEukaryotic genomesGram-negative bacteriaCellular functionsDifferent organismsGenetic approachesReading frameBiological roleProteomicsMicroproteinsEnable identificationProteinColiGenomeRecent advances