Reciprocal regulatory balance within the CLEC16A-RNF41 mitophagy complex depends on an intrinsically disordered protein region

CLEC16A is an E3 ubiquitin ligase that regulates mito-chondrial quality control through mitophagy and is associated with over 20 human diseases. CLEC16A forms a complex with another E3 ligase, RNF41, and a ubiquitin-specific peptidase, USP8; however, regions that regulate CLEC16A activity or the assembly of the tripartite mitophagy regulatory complex are unknown. Here, we report that CLEC16A contains an internal intrinsically disordered protein region (IDPR) that is crucial for CLEC16A function and turnover. IDPRs lack a fixed secondary structure and possess emerging yet still equivocal roles in protein stability, interactions, and enzymatic activity. We find that the internal IDPR of CLEC16A is crucial for its degrada-tion. CLEC16A turnover was promoted by RNF41, which binds and acts upon the internal IDPR to destabilize CLEC16A. Loss of this internal IDPR also destabilized the ubiquitin-dependent tripartite CLEC16A-RNF41-USP8 complex. Finally, the pres-ence of an internal IDPR within CLEC16A was confirmed using NMR and CD spectroscopy. Together, our studies reveal that an IDPR is essential to control the reciprocal regulatory bal-ance between CLEC16A and RNF41, which could be targeted to improve mitochondrial health in disease.

Automated summary

CLEC16A is an E3 ubiquitin ligase that plays a crucial role in regulating mitochondrial quality control through mitophagy and is associated with various human diseases. A recent study discovered an internal intrinsically disordered protein region (IDPR) within CLEC16A that is essential for its function and turnover. This IDPR is targeted by RNF41 to promote CLEC16A degradation and destabilize the CLEC16A-RNF41-USP8 complex. These findings highlight the importance of the IDPR in controlling the regulatory balance between CLEC16A and RNF41, which could be therapeutically targeted to improve mitochondrial health in disease.