|Coordinate||5,760,826 bp (GRCm38)|
|Base Change||C ⇒ A (forward strand)|
|Gene Name||SCY1-like 1 (S. cerevisiae)|
|Synonym(s)||2810011O19Rik, mfd, mdf, Ntkl, p105|
|Chromosomal Location||5,758,427-5,771,401 bp (-)|
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transcriptional regulator belonging to the SCY1-like family of kinase-like proteins. The protein has a divergent N-terminal kinase domain that is thought to be catalytically inactive, and can bind specific DNA sequences through its C-terminal domain. It activates transcription of the telomerase reverse transcriptase and DNA polymerase beta genes. The protein has been localized to the nucleus, and also to the cytoplasm and centrosomes during mitosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a spontaneous mutation or a knock-out allele develop a motoneuron disease characterized by gait ataxia, reduced grip strength, tremors, progressive hindlimb paralysis, muscular atrophy, and motoneuron degeneration. [provided by MGI curators]
|Amino Acid Change||Valine changed to Phenylalanine|
|Institutional Source||Beutler Lab|
|Gene Model||predicted gene model for protein(s): [ENSMUSP00000025890] [ENSMUSP00000080214]|
AA Change: V488F
|Predicted Effect||probably damaging
PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|Meta Mutation Damage Score||0.288|
|Is this an essential gene?||Probably essential (E-score: 0.940)|
|Candidate Explorer Status||CE: excellent candidate; human score: -0.5; ML prob: 0.702|
Linkage Analysis Data
|Alleles Listed at MGI|
|Mode of Inheritance||Unknown|
|Last Updated||2019-05-16 1:00 PM by Anne Murray|
|Record Created||2019-02-23 3:59 AM by Bruce Beutler|
The spartacus phenotype was identified among G3 mice of the pedigree R6625, some of which showed reduced body weights (Figure 1) as well as reduced time on a rotarod during a rotarod performance test (i.e., impaired coordination/motor capabilities) (Figure 2) compared to wild-type littermates. Some mice also showed ataxia (Figure 3).
|Nature of Mutation|
Whole exome HiSeq sequencing of the G1 grandsire identified 34 mutations. Both of the above anomalies were linked to mutations in three genes on chromosome 19: Scyl1, Ppp1r32, and Olfr1441. The mutation in Scyl1 was presumed causative as mutations in Scy1l are known to cause phenotypes similar to those observed in the spartacus mice (see MGI). The Scyl1 mutation is a G to T transversion at base pair 5,760,826 (v38) on chromosome 19, or base pair 10,589 in the GenBank genomic region NC_000085. The strongest association was found with a recessive model of inheritance to the body weight phenotype, wherein two variant homozygotes departed phenotypically from 26 homozygous reference mice and 41 heterozygous mice with a P value of 4.888 x 10-11 (Figure 4).
The mutation corresponds to residue 1,551 in the mRNA sequence NM_023912 within exon 10 of 17 total exons.
The mutated nucleotide is indicated in red. The mutation results in a valine to phenylalanine substitution at position 488 (V488F) in the SCYL1 protein, and is strongly predicted by Polyphen-2 to cause loss of function (score = 0.999).
Scyl1 encodes Scy1-like 1 (SCYL1; alternatively, NTKL [N-terminal kinase-like] and p105), a member of the Scy1-like family of catalytically inactive protein kinases. SCYL1 has an N-terminal kinase-like domain. SCYL1 does not contain a kinase subdomain 1 (1;2). SCYL1 has three HEAT repeats and a coiled-coil. The HEAT repeats mediate SCYL1 oligomerization. SCYL1 has a C-terminal RKLD sequence that is similar to coatomer (COPI)-binding motifs in transmembrane ER proteins. The RKLD sequence mediates interactions with the appendage domain of the coatomer subunit γ-2 (alternatively, COPG2 or γ2-COP) (3).
SCYL1 undergoes alternative splicing to generate two variants that encode proteins of 791 (variant 1) and 707 (variant 2) amino acids (2). Variant 1 lacks half of exon 14, while variant 2 lacks most of exon 14, all of exon 15, and half of exon 16.
The spartacus mutation results in a valine to phenylalanine substitution at position 488 (V488F); Val488 is within an undefined region between the second and third HEAT repeats.
SCYL1 is ubiquitously expressed (1;2). SCYL1 is cytoplasmic and is localized at the interface between the Golgi apparatus and the membrane trafficking machinery mediated by coatomer (COPI)-coated vesicles (4).
The COPI complex has seven core subunits: α-COP, β’-COP, ε-COP, β-COP, δ-COP, γ-COP, and ζ-COP (5-8). The COPI complex, along with other vesicle machinery (e.g., clathrin and COPII), promotes selection of cargo for vesicle trafficking as well as vesicle formation. The COPI complex is required for sorting of lipids and proteins within the Golgi cisternae and between the ER and Golgi (9;10). The COPI complex also functions in maintaining ER- and Golgi-resident chaperones in their respective compartments, endosomal transport and function, regulating lipid droplet homeostasis, mRNA transport, and the breakdown of the nuclear envelope [reviewed in (11)]. The COPI complex prevents the cell-surface expression of unassembled, dysfunctional proteins. The COPI complex recognizes cargo based on the presence of sorting signals within the cytoplasmic domains of the proteins (e.g., di-lysine KKxx and KxKxx motifs; arginine-based ER retrieval signals [ɸRxR; in which ɸ represents any hydrophobic amino acid]). The outer-coat COPI subunits α and β’ interact with dilysine K(X)KXX cargo motifs, and the adaptor subunit γ interacts with p23 transmembrane peptides (12-15). COPI-coated vesicles also promote the transport of K/HDEL cargoes associated with specific receptors (16); transport of HDEL-associated cargoes is dependent on δ-COP (17).
During formation of the COPI-coated vesicle, the cytoplasmic coatomer is recruited to membrane by the GTPase Arf1, which also regulate recruitment of COPI and clathrin-adaptor proteins. The F-subcomplex interacts with Arf1, subsequently recruiting the COPI complex to Golgi membranes. In the absence of cargo, inactive GDP-bound Arf1, the F-subcomplex (closed conformation), and the B-subcomplex are located in the cytoplasm. Upon cargo recognition, the B-subcomplex is recruited. Arf1 activation, via GDP-GTP exchange, promotes recruitment of the F-subcomplex via the γ-COP and β-COP subunits. Upon recruitment, the F-subcomplex transitions to an open conformation via an unknown mechanism.
SCYL1 is putatively involved in intracellular transport processes.
SCYL1 interacts with components of COPI coats (e.g., b-COP and γ-COP) to regulate COPI-mediated retrograde protein trafficking at the interface between the Golgi apparatus and the ER (3;4). RNAi-mediated SCYL1 knockdown resulted in aberrant COPI-mediated retrograde traffic of the KDEL receptor to the ER; anterograde trafficking was not affected (4). SCYL1 also interacts with class II ARFs (e.g., ARF4) to link the class II ARFs to γ2-bearing COPI subcomplexes (3).
SCYL1 is also a cytoplasmic component of the mammalian nuclear tRNA export machinery (18). SCYL1 binds tRNA and associates with the cytoplasmic side of the nuclear pore complex component Nup98 (18). SCYL1 also interacts with components of the nuclear tRNA export machinery (i.e., Xpo-t, Xpo-5, and Ran) (18). SCYL1 also putatively unloads the aminoacyl-tRNAs from the nuclear tRNA export receptor at the cytoplasmic side of the nuclear pore complex and channels them to the eukaryotic elongation factor eEF-1A for use in protein synthesis (18).
Mutations in SCYL1 are linked to cases of autosomal recessive spinocerebellar ataxia-21 (OMIM: #616719) (19;20). Patients with autosomal recessive spinocerebellar ataxia-21 show early childhood-onset of cerebellar ataxia associated with cerebellar atrophy. Patients also have recurrent liver failure episodes in the first decade of life, leading to chronic liver fibrosis and later-onset peripheral neuropathy. Some patients also show mild learning disabilities. Mutations in SCYL1 can cause recurrent early-onset low γ-glutamyl-transferase cholestasis, acute liver failure, and neurodegeneration (i.e., CALFAN syndrome) (21;22).
Scyl1-deficient (Scyl1-/-) mice showed early-onset progressive motor neuron disease with growth retardation/reduced body weights, abnormal gait (waddling), muscle wasting, reduced grip strength, and paralysis of the hind paws (23;24). Muscles from the Scyl1-/- mice showed neurogenic atrophy, fiber type switching, and disuse atrophy (23). Scyl1-/- peripheral nerves showed axonal degeneration and segmental demyelination (23). Scyl1-/- mice showed a reduction in spinal ventral horn motor neuron numbers and evidence of inflammation (23). Homozygous Scyl1 mutant mice (the ‘muscle deficient’ [mdf] model) showed reduced body sizes and fertility, progressive neuromuscular atrophy, progressive reduction of forelimb grip strength, hindlimb paralysis, gait ataxia, abnormal hindlimb posture, and tremors (25-27). The mice also showed cerebellar atrophy, Purkinje cell loss, and optic nerve atrophy (27).
The phenotypes observed in the spartacus mice indicates loss of SCYL1-associated function.
spartacus(F):5'- TTAAAGGCCTGTGGAGTAGC -3'
spartacus(R):5'- TTTTAGACCTTGGTTGGCCC -3'
spartacus_seq(F):5'- CAGCACTTCCAGGGTGTG -3'
spartacus_seq(R):5'- CCTGCCCTGGGAAGTGGAAAG -3'
1. Liu, S. C., Lane, W. S., and Lienhard, G. E. (2000) Cloning and Preliminary Characterization of a 105 kDa Protein with an N-Terminal Kinase-Like Domain. Biochim Biophys Acta. 1517, 148-152.
2. Kato, M., Yano, K., Morotomi-Yano, K., Saito, H., and Miki, Y. (2002) Identification and Characterization of the Human Protein Kinase-Like Gene NTKL: Mitosis-Specific Centrosomal Localization of an Alternatively Spliced Isoform. Genomics. 79, 760-767.
3. Hamlin, J. N., Schroeder, L. K., Fotouhi, M., Dokainish, H., Ioannou, M. S., Girard, M., Summerfeldt, N., Melancon, P., and McPherson, P. S. (2014) Scyl1 Scaffolds Class II Arfs to Specific Subcomplexes of Coatomer through the Gamma-COP Appendage Domain. J Cell Sci. 127, 1454-1463.
4. Burman, J. L., Bourbonniere, L., Philie, J., Stroh, T., Dejgaard, S. Y., Presley, J. F., and McPherson, P. S. (2008) Scyl1, Mutated in a Recessive Form of Spinocerebellar Neurodegeneration, Regulates COPI-Mediated Retrograde Traffic. J Biol Chem. 283, 22774-22786.
5. Dodonova, S. O., Diestelkoetter-Bachert, P., von Appen, A., Hagen, W. J., Beck, R., Beck, M., Wieland, F., and Briggs, J. A. (2015) VESICULAR TRANSPORT. A Structure of the COPI Coat and the Role of Coat Proteins in Membrane Vesicle Assembly. Science. 349, 195-198.
6. Dodonova, S. O., Aderhold, P., Kopp, J., Ganeva, I., Rohling, S., Hagen, W. J. H., Sinning, I., Wieland, F., and Briggs, J. A. G. (2017) 9A Structure of the COPI Coat Reveals that the Arf1 GTPase Occupies Two Contrasting Molecular Environments. Elife. 6, 10.7554/eLife.26691.
7. Waters, M. G., Serafini, T., and Rothman, J. E. (1991) 'Coatomer': A Cytosolic Protein Complex Containing Subunits of Non-Clathrin-Coated Golgi Transport Vesicles. Nature. 349, 248-251.
8. Lowe, M., and Kreis, T. E. (1998) Regulation of Membrane Traffic in Animal Cells by COPI. Biochim Biophys Acta. 1404, 53-66.
9. Lee, M. C., Miller, E. A., Goldberg, J., Orci, L., and Schekman, R. (2004) Bi-Directional Protein Transport between the ER and Golgi. Annu Rev Cell Dev Biol. 20, 87-123.
10. Bethune, J., Wieland, F., and Moelleken, J. (2006) COPI-Mediated Transport. J Membr Biol. 211, 65-79.
11. Arakel, E. C., and Schwappach, B. (2018) Formation of COPI-Coated Vesicles at a Glance. J Cell Sci. 131, 10.1242/jcs.209890.
12. Jackson, L. P., Lewis, M., Kent, H. M., Edeling, M. A., Evans, P. R., Duden, R., and Owen, D. J. (2012) Molecular Basis for Recognition of Dilysine Trafficking Motifs by COPI. Dev Cell. 23, 1255-1262.
13. Ma, W., and Goldberg, J. (2013) Rules for the Recognition of Dilysine Retrieval Motifs by Coatomer. EMBO J. 32, 926-937.
14. Cosson, P., and Letourneur, F. (1994) Coatomer Interaction with Di-Lysine Endoplasmic Reticulum Retention Motifs. Science. 263, 1629-1631.
15. Harter, C., and Wieland, F. T. (1998) A Single Binding Site for Dilysine Retrieval Motifs and p23 within the Gamma Subunit of Coatomer. Proc Natl Acad Sci U S A. 95, 11649-11654.
16. Majoul, I., Straub, M., Hell, S. W., Duden, R., and Soling, H. D. (2001) KDEL-Cargo Regulates Interactions between Proteins Involved in COPI Vesicle Traffic: Measurements in Living Cells using FRET. Dev Cell. 1, 139-153.
17. Arakel, E. C., Richter, K. P., Clancy, A., and Schwappach, B. (2016) Delta-COP Contains a Helix C-Terminal to its Longin Domain Key to COPI Dynamics and Function. Proc Natl Acad Sci U S A. 113, 6916-6921.
18. Chafe, S. C., and Mangroo, D. (2010) Scyl1 Facilitates Nuclear tRNA Export in Mammalian Cells by Acting at the Nuclear Pore Complex. Mol Biol Cell. 21, 2483-2499.
19. Schmidt, W. M., Rutledge, S. L., Schule, R., Mayerhofer, B., Zuchner, S., Boltshauser, E., and Bittner, R. E. (2015) Disruptive SCYL1 Mutations Underlie a Syndrome Characterized by Recurrent Episodes of Liver Failure, Peripheral Neuropathy, Cerebellar Atrophy, and Ataxia. Am J Hum Genet. 97, 855-861.
20. Shohet, A., Cohen, L., Haguel, D., Mozer, Y., Shomron, N., Tzur, S., Bazak, L., Basel Salmon, L., and Krause, I. (2019) Variant in SCYL1 Gene Causes Aberrant Splicing in a Family with Cerebellar Ataxia, Recurrent Episodes of Liver Failure, and Growth Retardation. Eur J Hum Genet. 27, 263-268.
21. Lenz, D., McClean, P., Kansu, A., Bonnen, P. E., Ranucci, G., Thiel, C., Straub, B. K., Harting, I., Alhaddad, B., Dimitrov, B., Kotzaeridou, U., Wenning, D., Iorio, R., Himes, R. W., Kuloglu, Z., Blakely, E. L., Taylor, R. W., Meitinger, T., Kolker, S., Prokisch, H., Hoffmann, G. F., Haack, T. B., and Staufner, C. (2018) SCYL1 Variants Cause a Syndrome with Low Gamma-Glutamyl-Transferase Cholestasis, Acute Liver Failure, and Neurodegeneration (CALFAN). Genet Med. 20, 1255-1265.
22. Spagnoli, C., Frattini, D., Salerno, G. G., and Fusco, C. (2018) On CALFAN Syndrome: Report of a Patient with a Novel Variant in SCYL1 Gene and Recurrent Respiratory Failure. Genet Med. .
23. Pelletier, S., Gingras, S., Howell, S., Vogel, P., and Ihle, J. N. (2012) An Early Onset Progressive Motor Neuron Disorder in Scyl1-Deficient Mice is Associated with Mislocalization of TDP-43. J Neurosci. 32, 16560-16573.
24. Kuliyev, E., Gingras, S., Guy, C. S., Howell, S., Vogel, P., and Pelletier, S. (2018) Overlapping Role of SCYL1 and SCYL3 in Maintaining Motor Neuron Viability. J Neurosci. .
25. Womack, J. E., MacPike, A., and Meier, H. (1980) Muscle Deficient, a New Mutation in the Mouse. J Hered. 71, 68.
26. Blot, S., Poirier, C., and Dreyfus, P. A. (1995) The Mouse Mutation Muscle Deficient (Mdf) is Characterized by a Progressive Motoneuron Disease. J Neuropathol Exp Neurol. 54, 812-825.
27. Schmidt, W. M., Kraus, C., Hoger, H., Hochmeister, S., Oberndorfer, F., Branka, M., Bingemann, S., Lassmann, H., Muller, M., Macedo-Souza, L. I., Vainzof, M., Zatz, M., Reis, A., and Bittner, R. E. (2007) Mutation in the Scyl1 Gene Encoding Amino-Terminal Kinase-Like Protein Causes a Recessive Form of Spinocerebellar Neurodegeneration. EMBO Rep. 8, 691-697.
|Science Writers||Anne Murray|
|Illustrators||Diantha La Vine|
|Authors||Nanda Regmi, Zhao Zhang, Lauren Prince, Jamie Russell, and Bruce Beutler|