Abstract
Background: Protein ubiquitination is a key post-translational modification that governs protein stability and cellular homeostasis. KLHDC3 is a substrate recognition receptor in the recently identified C-terminal degron-mediated DesCEND ubiquitination pathway. It selectively binds proteins with C-terminal RxxxG motifs, targeting them for degradation. While N-terminal degron pathways are well-characterized, the physiological roles of C-terminal degrons remain poorly understood. To explore KLHDC3’s function in a physiological context, we generated mice deficient in the Klhdc3 gene. Results: Klhdc3-deficient mice exhibited sub-Mendelian birth rates and progressive postnatal lethality, with a median survival of 136 days and a maximum lifespan of approximately one year. Surviving mice showed early growth retardation followed by normalization of body mass, and later developed pronounced obesity, with some individuals reaching fat mass levels exceeding 50% of total body weight. Transcriptomic and proteomic analyses of Klhdc3−/− embryonic fibroblasts revealed significant changes in protein expression with minimal alterations in transcript levels, consistent with KLHDC3’s role in post-translational regulation. Among the upregulated proteins, HINT1 was identified as a novel KLHDC3 substrate containing a C-terminal degron motif. Protein stability assays and immunoblotting confirmed HINT1 as a candidate target of KLHDC3. Conclusions: This study establishes a physiological role for the DesCEND pathway in vivo and identifies KLHDC3 as a critical regulator of development, survival, and adiposity in mice. The identification of HINT1 as a putative KLHDC3 substrate expands our understanding of C-terminal degron-mediated protein regulation and suggests broader implications for developmental and metabolic processes. Supplementary Information: The online version contains supplementary material available at 10.1186/s12864-026-12574-5.