Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1

Regulation of metabolic enzymes through degradation by the ubiquitin-proteosome system regulation is essential towards maintenance of cellular homeostasis. Our approach directly addresses a problem in the field; linking metabolic signal to an E3 ligase response. We employ active E3 ligase profiling coupled with broad MS-based screening, to reveal the changes in the proteome and E3 ligase-ome in response to the starvation or excess of a specific metabolite. We then use computationally driven strategies to connect these responses before in vitro and in cellulo reconstitution. The application of this strategy on cysteine metabolism led to our finding of LRRC58 mediated control of CDO1 degradation. Through reconstitution of this system, we also reveal that endogenous CDO1 degradation by LRRC58 is distinct from degradation induced by a molecular glue. Additionally, we have visualized CDO1 ubiquitylation by an LRRC58 CRL through cryo-EM, demonstrating the structural basis for CDO1 targeting by LRRC58.