2020
Non-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
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 ResearchMeSH KeywordsCold Shock Proteins and PeptidesEscherichia coliMolecular Sequence AnnotationProteinsProteomicsConceptsCold 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