title: Proteomic survey of ubiquitin-linked nuclear proteins in interferon-stimulated macrophages.
abstract: Ubiquitin modification plays a critical role in immune responses. Some cytoplasmic factors require ubiquitination to execute proper signaling upon pathogen and cytokine stimulation. However, ubiquitin modification and its functional significance have not been fully studied for many nuclear proteins. We report here that stimulation of RAW macrophages with interferon-γ and toll-like receptor ligands that activates innate immune responses triggers a global increase in ubiquitinated proteins in the nucleus, pointing to the role for ubiquitin modification in regulating nuclear events during innate immune responses. By immunopurification and mass-spectrometry analyses, we found that more than 200 proteins are directly or indirectly associated with ubiquitin in stimulated RAW cells. These proteins included proteins in the ubiquitin pathways, those involved in DNA metabolism, chromatin and transcriptional regulation, and mRNA processing. The largest group of proteins found in our list was ribosomal proteins important for protein translation. Other proteins found here were heat shock proteins and stress-response factors, suggesting a link between macrophage activation and stress response. In conclusion, upon macrophage activation, a large number of nuclear proteins become associated with ubiquitin modification, presumably leading to a global shift in the genome activity, important for proper execution of innate immune responses.
authors.affiliation: Program of Genomics in Differentiation, Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, Bethesda, Maryland, USA.
authors.forename: Ji Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Eric D
authors.initials: ED
authors.lastname: Anderson
authors.forename: Walter
authors.initials: W
authors.lastname: Huynh
authors.forename: Anup
authors.initials: A
authors.lastname: Dey
authors.forename: Keiko
authors.initials: K
authors.lastname: Ozato
mesh_terms: D000818:Animals; D002460:Cell Line; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects / Q000502:physiology; D006360:Heat-Shock Proteins / Q000378:metabolism; D006801:Humans; D007113:Immunity, Innate / Q000502:physiology; D007371:Interferon-gamma / Q000494:pharmacology*; D008262:Macrophage Activation / Q000187:drug effects; D008264:Macrophages / Q000187:drug effects / Q000276:immunology / Q000378:metabolism* / Q000473:pathology; D051379:Mice; D009687:Nuclear Proteins / Q000378:metabolism*; D009838:Oligodeoxyribonucleotides / Q000494:pharmacology; D014176:Protein Biosynthesis / Q000187:drug effects / Q000502:physiology; D040901:Proteomics; D013312:Stress, Physiological / Q000187:drug effects / Q000502:physiology; D051193:Toll-Like Receptors / Q000819:agonists; D054875:Ubiquitination / Q000187:drug effects
chemical_list: D006360:Heat-Shock Proteins; D009687:Nuclear Proteins; D009838:Oligodeoxyribonucleotides; D051193:Toll-Like Receptors; D007371:Interferon-gamma