A conformation-dependent hydrophobic degron determines Rab9a-mediated vesicular trafficking

The small GTPase Rab9 plays a major role in the vesicular trafficking of cation-independent mannose-6-phosphate receptor (CI-M6PR). CI-M6PR trafficking has also been reported to be perturbed by the dysfunction of a ubiquitin ligase necessary for protein quality control (PQC). However, the mechanism underlying the participation of the PQC machinery in CI-M6PR trafficking is poorly understood. In this study, we found an extremely short half-life of GDP-bound Rab9, which is in clear contrast to its phylogenetically closest relative, Rab7. Comparison of the amino acid sequences of these relatives revealed that hydrophobic residues are specifically exposed in the switch I region of Rab9a and that these residues are recognized by the PQC machinery. We defined this exposed hydrophobicity as a conformation-dependent hydrophobic (CDH) degron because its existence determines the instability of Rab proteins in a nucleotide-dependent manner. CDH degron-mediated instability is essential for Rab9a function, given that forced accumulation of CDH degron-mutated Rab9a in cells resulted in the defective localization of CI-M6PR, a similar phenotype observed in PQC dysfunction. Thus, the CDH degron-driven PQC system is necessary for the proper vesicular trafficking of CI-M6PR. We also identified valosin-containing protein/p97 as a CDH degron-dependent PQC factor for GDP-bound Rab9a.