Revealing site-specific crosstalk between SUMO-Ubiquitin across the human proteome

Different post transnational modifications (PTMs) may act in concert to modulate protein activity and function. Intramolecular crosstalk between PTMs on the same protein provides another level of complexity affecting protein life-cycle. Yet, regulatory principles involved in the dynamic regulation of PTMs remain largely unexplored. Here, we computationally mapped reported lysine modification sites across the human proteome and found hundreds of sites that can be targeted by either ubiquitin or SUMO, which we defined as Sites of Alternative Modification (SAM). Although only a handful of proteins were previously experimentally validated to contain specific lysines that were competitively targeted both by ubiquitin and SUMO, our analysis revealed more than 200 novel substrates bearing SAM motif. Numerous components of signaling pathways and transcription/translation factors were overrepresented in SAM proteins. Multi-omic analysis of the proteins containing Ubiquitin-SUMO SAMs were associated with the ability to switch between cytosolic and nuclear compartments and a distinct protein expression signature across human tissues. Thus, our analysis provides an important resource to the scientific community, suggesting SAMs as a novel regulatory motif by which the fate of proteins may be altered. Lastly, our approach may be broadly applicable to reveal insight about the PTM landscape in various processes ranging from the regulation of the ubiquitin system to proteostasis control.