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 modelPolypeptideNucleoliExpression
2021
Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates
Na Z, Luo Y, Cui DS, Khitun A, Smelyansky S, Loria JP, Slavoff SA. Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates. Journal Of The American Chemical Society 2021, 143: 12675-12687. PMID: 34346674, PMCID: PMC8564862, DOI: 10.1021/jacs.1c05386.Peer-Reviewed Original ResearchConceptsMembraneless organellesSmall open reading framesP-body dynamicsLiquid-liquid phase separationOpen reading frameGrowth factor signalingPresence of RNAEvolutionary conservationP-bodiesCellular processesCell divisionReading frameProteogenomic identificationFactor signalingMacromolecular complexesBiomolecular condensatesSecondary structureAmino acidsCell growthMicroproteinsPhosphorylationCell proliferationOrganellesBiophysical processesProliferation
2020
The NBDY Microprotein Regulates Cellular RNA Decapping
Na Z, Luo Y, Schofield JA, Smelyansky S, Khitun A, Muthukumar S, Valkov E, Simon MD, Slavoff SA. The NBDY Microprotein Regulates Cellular RNA Decapping. Biochemistry 2020, 59: 4131-4142. PMID: 33059440, PMCID: PMC7682656, DOI: 10.1021/acs.biochem.0c00672.Peer-Reviewed Original ResearchConceptsP-bodiesNonsense-mediated decay factorsKO cellsSmall open reading framesCytoplasmic ribonucleoprotein granulesOpen reading frameSubstrate transcriptsCellular transcriptomeRibonucleoprotein granulesTarget transcriptsRNA stabilityKnockout cellsUTR lengthReading frameGlobal profilingProteogenomic identificationMacromolecular complexesHuman RNACellular RNACytoplasmic RNAGene stabilityAmino acidsCell growthMicroproteinsTranscriptsNon-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 thousandsEukaryotesProkaryotes
2019
Proteomic Detection and Validation of Translated Small Open Reading Frames
Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Current Protocols In Chemical Biology 2019, 11: e77. PMID: 31750990, PMCID: PMC6878975, DOI: 10.1002/cpch.77.Peer-Reviewed Original ResearchConceptsSiRNA-based silencingSmall open reading framesNon-AUG start codonsOpen reading frameStandard proteomic methodsSpecific transcript isoformsCultured human cellsUnique tryptic peptidesGenomic lociShorter proteinTranscript isoformsProtein databaseProteomic methodsNovel regulatorReading frameProteomic detectionStart codonFunctional characterizationMass spectrometry-based detectionComplete annotationSmall proteinsHuman cellsTryptic peptidesProtein extractionSmORFsSmall open reading frames and cellular stress responses
Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Molecular Omics 2019, 15: 108-116. PMID: 30810554, PMCID: PMC6662920, DOI: 10.1039/c8mo00283e.Peer-Reviewed Original ResearchConceptsSmall open reading framesOpen reading frameUpstream ORFsReading frameStress responseCellular stress responseEukaryotic cellsGenome annotationCellular homeostasisDownstream cistronEvolutionary spaceFunctional polypeptidesAmino acidsEukaryotesSmORFsPolypeptideProkaryotesGenomeCistronGenomicsORFRecent advancesProteomicsFootprintingRegulator
2017
Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein
Yuan P, D’Lima N, Slavoff SA. Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein. Biochemistry 2017, 57: 56-60. PMID: 29039649, PMCID: PMC5761644, DOI: 10.1021/acs.biochem.7b00864.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, High Pressure LiquidEscherichia coliEscherichia coli K12Escherichia coli ProteinsGene Expression Regulation, BacterialGreen Fluorescent ProteinsHeat-Shock ProteinsHeat-Shock Proteins, SmallHeat-Shock ResponseMembrane ProteinsModels, MolecularMolecular Sequence AnnotationOpen Reading FramesPhosphogluconate DehydrogenaseProtein Conformation, alpha-HelicalProtein Interaction Domains and MotifsProtein TransportProteogenomicsProteomicsRecombinant Fusion ProteinsTandem Mass SpectrometryConceptsHeat shock proteinsShock proteinsMembrane proteomicsE. coli heat shock proteinsComparative membrane proteomicsSmall open reading framesMembrane protein enrichmentQuantitative membrane proteomicsQuantitative proteomics protocolBacterial stress responseQuantitative mass spectrometryOpen reading frameDiscovery of thousandsEscherichia coli K12Transmembrane helicesProteomics protocolMembrane proteinsEvolutionary spaceReading frameSmall proteinsStress responseProteomicsColi K12Amino acidsProtein enrichmentComparative 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