K48 ubiquitin selectively targets oxidized proteins in vivo

Ubiquitin is a highly conserved eukaryotic protein responsible for regulating a variety of functions when conjugated to target proteins. Ubiquitin is essential, accumulates during the stress response, and is the canonical signal for protein degradation by the proteasome. Still, the function of ubiquitin in response to oxidative stress, particularly in the removal of oxidized proteins remains elusive because of the number of potential targets and different roles that polyubiquitin chains can play. Since polyubiquitin chains linked by K48 ubiquitin are the most abundant and canonical signal for protein degradation, we investigated the roles of K48 ubiquitin in the degradation of oxidized proteins. Combining protein oxidation, linkage-specific ubiquitination screens, and quantitative proteomics, we found K48 ubiquitin accumulated in a bimodal fashion, at both the early and late phase of response. We further showed that a fraction of oxidized proteins are conjugated with K48 ubiquitin in vivo. Using quantitative proteomics we identified ~750 ubiquitinated proteins and ~400 oxidized proteins that were differentially modified during the stress response, and around half the proteins were both oxidized and ubiquitinated. These proteins were highly abundant and function in translation and energy metabolism. Finally, we showed that the ubiquitination system is required for degradation of oxidized proteins, suggesting that oxidized proteins that rapidly accumulate during stress are ubiquitinated, and degraded during the later recovery phase. This temporal disconnect may be necessary for reprogramming protein dynamics, restoring proteostasis, and resuming cell growth.