Scyl1, Mutated in a Recessive Form of Spinocerebellar Neurodegeneration, Regulates COPI-mediated Retrograde Traffic

Abstract

Scy1-like 1 (Scyl1), a member of the Scy1-like family of catalytically inactive protein kinases, was recently identified as the gene product altered in muscle-deficient mice, which suffer from motor neuron degeneration and cerebellar atrophy. To determine the function of Scyl1, we have now used a mass spectrometry-based screen to search for Scyl1-binding partners and identified components of coatomer I (COPI) coats. The interaction was confirmed in pull-down assays, and Scyl1 co-immunoprecipitates with ␤COP from brain lysates. Interestingly, and unique for a non-transmembrane domain protein, Scyl1 binds COPI coats using a C-terminal RKLD-COO ؊ sequence, similar to the KKXX-COO ؊ COPI-binding motif found in transmembrane endoplasmic reticulum (ER) proteins. Scyl1 co-localizes with ␤COP and is localized, in an Arf1-independent manner, to the ER-Golgi intermediate compartment and the cis-Golgi, sites of COPI-mediated membrane budding. The localization and binding properties of Scyl1 strongly suggest a function in COPI transport, and inhibitory RNA-mediated knock down of the protein disrupts COPI-mediated retrograde traffic of the KDEL receptor to the ER without affecting anterograde traffic from the ER. Our data demonstrate a function for Scyl1 as an accessory factor in COPI trafficking and suggest for the first time that alterations in the COPI pathway result in neurodegenerative disease.The murine autosomal recessive neurodegenerative disease model "muscle-deficient" (mdf) displays clinical and histological features indicative of a progressive motor neuropathy (1). Homozygotes develop a posterior waddle at 4 -8 weeks of age followed by hind limb paralysis and forelimb weakness (1). Skeletal muscles exhibit a neurogenic atrophy, and there is progressive neurodegeneration of lower motor neurons (1, 2). Among the murine neuromuscular atrophies, the motor neuron degeneration in mdf is most similar to that seen in wobbler (1). Interestingly, mdf also suffers from symptoms indicative of cerebellar involvement including gait ataxia, abnormal hind limb posture, and tremor (3). Therefore, mdf appears to be linked to both neuromuscular atrophy and spinocerebellar ataxia and is thus an animal model for neuromuscular disease with cerebellar involvement in humans.Most recently, null mutations in the Scy1-like 1 (Scyl1) gene were determined to be responsible for the pathology seen in the mdf mouse (3). Scyl1 was initially identified as a ubiquitously expressed member of the Scy1-like family of protein kinases (4) and is a distant homologue of Scy1-like 2/CVAK104 (coated vesicle-associated kinase of 104 kDa), which is involved in the trafficking of clathrin-coated vesicles (CCVs) 3 (5-7). Scy1-like kinases are thought to be kinase-inactive as they lack several highly conserved residues essential for catalytic activity (8, 9). Scyl1 was indirectly implicated in clathrin-mediated endocytosis when it was identified as an in vitro binding partner for the ␣-and ␤2-ear domains of the clathrin adaptor protein-2 (AP-2) (in this study, ...

Scyl1 scaffolds class II Arfs to selective subcomplexes of coatomer via the γ-COP appendage domain

“…Scyl1 binds COPI primarily through a dibasic cargo-like motif (RKLD-COO 2 ) at the extreme C-terminus (Ma and Goldberg, 2013), but a C-terminal coiledcoil domain also contributes to binding (Burman et al, 2008). We thus took advantage of the Scyl1 truncation mutant GST-Scyl1 1-750 ( Fig.…”

“…We thus took advantage of the Scyl1 truncation mutant GST-Scyl1 1-750 ( Fig. 3E), which does not bind COPI (Burman et al, 2008), to test the potential involvement of COPI in mediating the interaction between Scyl1 and Arf4. Whereas full-length GSTScyl1 (1-806) interacted with both Arf4-GFP and endogenous b-COP in lysates from Arf4-GFP-transfected cells, GST-Scyl1 1-750 retained full Arf4 interaction but showed no b-COP binding (Fig.…”

“…HEK-293T cells were transfected with FLAG-Scyl1 349-806 (a kinase-like-domain deletion construct), FLAG-Scyl1 547-806 [which removes the kinase-like domain and the HEAT repeats necessary for oligomerization (Fig. 5E)] or FLAG-Scyl1 fulllength RKRAA mutant [which reduces coatomer binding (Burman et al, 2008;Ma and Goldberg, 2013)]. GST-c2-appendage bound the kinase-deletion protein with the same enrichment as full-length Scyl1 (Fig.…”

“…We demonstrated previously that knockdown of Scyl1 disrupts trafficking of some forms of cargo from the cis-Golgi to the ER (Burman et al, 2008). To better define the mechanism of action of Scyl1, we now use GST-Scyl1 to perform affinity-selection of binding partners from tissue extracts, followed by protein identification by using mass spectrometry.…”

“…Scyl1, a member of the Scy1-like family of catalytically inactive protein kinases, was recently reported to function in retrograde COPI-mediated intracellular transport (Burman et al, 2008;Burman et al, 2010). Importantly, Scyl1 has also been identified as the gene product that is lost in an animal model of motor neuron disease, the muscle-deficient (mdf) mouse (Blot et al, 1995;Schmidt et al, 2007).…”