KCTD7 mutations impair the trafficking of lysosomal enzymes through CLN5 accumulation to cause neuronal ceroid lipofuscinoses

Abstract

Lysosomes are central organelles for cellular degradation and energy metabolism. Neuronal ceroid lipofuscinoses (NCLs) are a group of the most common neurodegenerative lysosomal storage disorders characterized by intracellular accumulation of ceroid in neurons. Mutations in KCTD7 , a gene encoding an adaptor of the CUL3-RING E3 ubiquitin ligase (CRL3) complex, are categorized as a unique NCL subtype. However, the underlying mechanisms remain elusive. Here, we report various lysosomal and autophagic defects in KCTD7-deficient cells. Mechanistically, the CRL3-KCTD7 complex degrades CLN5, whereas patient-derived KCTD7 mutations disrupt the interaction between KCTD7-CUL3 or KCTD7-CLN5 and ultimately lead to excessive accumulation of CLN5. The accumulated CLN5 disrupts the interaction between CLN6/8 and lysosomal enzymes at the endoplasmic reticulum (ER), subsequently impairing ER-to-Golgi trafficking of lysosomal enzymes. Our findings reveal previously unrecognized roles of KCTD7-mediated CLN5 proteolysis in lysosomal homeostasis and demonstrate that KCTD7 and CLN5 are biochemically linked and function in a common neurodegenerative pathway.

Alphafold Predictions Provide Insights into the Structural Features of the Functional Oligomers of All Members of the KCTD Family

“…The structure of the related proteins and previously structurally uncharacterized KCTD7 and KCTD14 (sub-Cluster 5B), although pentameric, appears to be characterized by a different organization of the CTD region. Indeed, the five chains of the terminal domain of these proteins, whose deficiency, in particular that of KCTD7, has been associated with a progressive neurodegenerative disorder and epilepsy [ 37 , 38 , 39 ], associate forming a circle-like structure with a larger cavity compared to that found in the pentamers of the KCTDs of Clusters 1–4. Our predictions highlight the peculiar oligomerization properties of the members of Cluster 6 (KCTD10, KCTD13, and TNFAIP1), which are involved in important neurological pathologies including autism [ 6 , 7 , 40 , 41 ].…”

Recent insights into the networking of CLN genes and proteins in mammalian cells

“…This is supported by the binding of CLN3 to CLN5 in several mammalian cell lines (Table 1; Figure 2a) (Lyly et al, 2009; Vesa et al, 2002; Yasa et al, 2021). While CLN3 is not known to bind to any other CLN protein, CLN5 has also been reported to interact with PPT1, TPP1, CLN6, CLN8, and KCTD7 (Lyly et al, 2009; Vesa et al, 2002; Wang, Cao, et al, 2022). The binding between CLN5 and PPT1 supports work in HeLa cells showing that PPT1 regulates the intracellular trafficking of CLN5 via P1‐ATPase, a common interactor of PPT1 and CLN5 (Lyly et al, 2009).…”

“…Loss or mutation of KCTD7 affects PPT1, TPP1, CLN5, CTSD, GRN, and CTSF, which intriguingly, comprise the set of CLN proteins that are secreted (Bateman et al, 1990; Benussi et al, 2016; Huber, 2021; Hughes et al, 2014; Isosomppi et al, 2002; Kaakinen et al, 2007; Kohan et al, 2005; Oörni et al, 2004; Poole et al, 1973; Tanaka et al, 2017; Zhou et al, 1993). In several human cell lines, loss or knockdown of KCTD7 affects the amounts of PPT1, TPP1, CTSD, CTSF, and GRN in lysosomes, as well as the amount of CLN5 in whole cell lysates (Table 6) (Wang, Cao, et al, 2022). Loss or knockdown of KCTD7 also impacts the activities of TPP1 and CTSD (Wang, Cao, et al, 2022).…”

“…In several human cell lines, loss or knockdown of KCTD7 affects the amounts of PPT1, TPP1, CTSD, CTSF, and GRN in lysosomes, as well as the amount of CLN5 in whole cell lysates (Table 6) (Wang, Cao, et al, 2022). Loss or knockdown of KCTD7 also impacts the activities of TPP1 and CTSD (Wang, Cao, et al, 2022). However, the primary role of KCTD7 appears to be regulating the amount of CLN5 within cells.…”

“…CLN6 and CLN8 localize to the membrane of the endoplasmic reticulum (ER) where they regulate lysosomal enzyme recruitment and lysosome biogenesis (Bajaj et al, 2020; Lonka et al, 2000; Mole et al, 2004). Finally, DnaJ homolog subfamily C member 5 (DNAJC5) and potassium channel tetramerization domain‐containing protein 7 (KCTD7) are peripheral membrane proteins that regulate misfolding‐associated protein secretion and protein degradation, respectively (Azizieh et al, 2011; Johnson et al, 2010; Lee et al, 2023; Wang, Cao, et al, 2022).…”