Visualization of ubiquitin conjugates using ubiquitin-mediated fluorescence complementation analysis

Ubiquitin-family peptide conjugation regulates the functions and stabilities of many proteins. Numerous cellular proteins are modified by covalent conjugation of ubiquitin-family peptides to specific lysine residues. These modifications provide a flexible means for regulating the properties of the substrate proteins. Because ubiquitin can be conjugated to substrate proteins at many different sites and in many topological configurations, these modifications have the potential to confer a wide range of functional states to the modified proteins. Ubiquitin conjugation is typically detected by immunoprecipitation of a putative substrate protein followed by immunoblotting to detect ubiquitin conjugated to the substrate. However, this assay cannot be used to detect ubiquitin conjugates in live cells. It is also difficult to determine the subcellular distribution of a specific ubiquitin conjugate using this approach. To visualize ubiquitin conjugates in live cells, we have developed the ubiquitin-mediated fluorescence complementation assay, which is based on the association of fragments of fluorescent proteins when ubiquitin fused to one fragment is conjugated to a substrate protein fused to a complementary fragment. This protocol focuses on the visualization of ubiquitin conjugated in cultured mammalian cells, but it can be adapted to any cell type or aerobically grown organism that can be genetically modified to express the fusion proteins.