The SNUPN gene encodes snurportin-1, a key adaptor protein important for nuclear import of small nuclear ribonucleoproteins (snRNPs), which are essential components of the spliceosome (summary by Nashabat et al., 2024).

The nuclear import of the spliceosomal snRNPs U1, U2, U4 and U5 is dependent on the presence of a complex nuclear localization signal (NLS). The latter is composed of the 5-prime-2,2,7-terminal trimethylguanosine (m3G) cap structure of the U snRNA and the Sm core domain.

Huber et al. (1998) described the isolation and cDNA cloning of a 45-kD protein, termed snurportin-1, which interacts specifically with m3G-cap but not m7G-cap structures. Snurportin-1 enhanced the m3G-cap-dependent nuclear import of U snRNPs in both Xenopus laevis oocytes and digitonin-permeabilized HeLa cells, demonstrating that it functions as an snRNP-specific nuclear import receptor. The m3G-cap and not the Sm core NLS appeared to be recognized by snurportin-1, indicating that at least 2 distinct import receptors interact with the complex snRNP NLS. Snurportin-1 is a nuclear import receptor which contains an N-terminal importin-beta-binding (IBB) domain, essential for function, and a C-terminal m3G-cap-binding region with no structural similarity to the arm repeat domain of importin-alpha (KPNA2; 600685). Using a UV cross-linking assay, Huber et al. (1998) identified snurportin-1 as a protein capable of binding m3G-cap. The protein was isolated, fragmented into peptides, and microsequenced. Corresponding ESTs were identified from online databases, and assembled into a full-length cDNA predicted to encode a 360-amino acid protein with a molecular weight of 41 kD.

Narayanan et al. (2002) reported that a mutant snurportin construct lacking the IBB domain, but containing an intact TMG cap-binding domain, localized primarily to the nucleus, whereas full-length snurportin localized to the cytoplasm. Snurportin interacted with SMN (600354), Gemin3 (606168), Sm snRNPs, and importin-beta (602738). In the presence of ribonucleases, the interactions with SMN and Sm proteins were abolished, suggesting that snRNAs may mediate this interplay. Cell fractionation studies showed that snurportin bound preferentially to cytoplasmic SMN complexes. Additionally, SMN directly interacted with importin-beta in a GST-pull-down assay, suggesting that the SMN complex may represent the Sm core NLS receptor predicted by previous studies. The authors concluded that, following Sm protein assembly, the SMN complex may persist until the final stages of cytoplasmic snRNP maturation, and may provide somatic cell RNPs with an alternative NLS.

Crystal Structure

Dong et al. (2009) presented a 2.9-angstrom resolution crystal structure of CRM1 (602559) bound to snurportin-1. Snurportin-1 binds CRM1 in a bipartite manner by means of an N-terminal leucine-rich nuclear export signal (LR-NES) and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between 2 CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues, and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin-1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.

Monecke et al. (2009) presented the crystal structure of the SPN1-CRM1-RanGTP (see 601179) export complex at 2.5-angstrom resolution. SPN1 is a nuclear import adaptor for cytoplasmically assembled, m3G-capped spliceosomal U snRNPs. The structure showed how CRM1 can specifically return the cargo-free form of SPN1 to the cytoplasm. The extensive contact area includes 5 hydrophobic residues at the SPN1 amino terminus that dock into a hydrophobic cleft of CRM1, as well as numerous hydrophilic contacts of CRM1 to m3G cap-binding domain and carboxyl-terminal residues of SPN1. Monecke et al. (2009) concluded that RanGTP promotes cargo binding to CRM1 solely through long-range conformational changes in the exportin.

In 18 patients from 15 unrelated families with autosomal recessive limb-girdle muscular dystrophy-29 (LGMDR29; 620793), Nashabat et al. (2024) identified homozygous or compound heterozygous mutations in the SNUPN gene (see, e.g., 607902.0001-607902.0004). The patients were ascertained through international collaboration, including the GeneMatcher Program, after exome sequencing identified biallelic SNUPN mutations. The mutations segregated with the disorder in 9 families; segregation studies for the other 6 families could not be performed. Nine mutations were identified: 2 missense, 4 nonsense, 2 frameshift, and 1 splice site. Eight of the 9 variants clustered in the last coding exon (exon 9) of the gene and were predicted to alter the C terminus; 1 variant (R55Q; 607902.0004) was located at a conserved residue in the N terminus. Fibroblasts derived from 5 patients from 4 families (F1, F2, F4, and F10) showed normal amounts of SNUPN mRNA transcripts, but total protein levels were decreased in all except the cells from F10 with the R55Q mutation. Detailed in vitro studies of patient-derived cells (fibroblasts and muscle cells), HeLa and HEK293 cells transfected with some of the mutations, and CRISPR/Cas9-mediated SNUPN-deficient mutant cell lines showed that the C terminus is important for SNUPN self-assembly and proper stability and function of SNUPN oligomers. Immunofluorescence studies of fibroblasts and muscle samples from some of the patients showed mislocalization of mutant SNUPN with increased perinuclear accumulation and abnormal retention in the cytoplasm, decreased protein levels in the nuclei, impaired nuclear import of snRNPs, and disruption of spliceosome maturation and function, resulting in aberrations of mRNA splicing and dysregulation of multiple genes, including those related to muscle structure and function and the extracellular matrix. The cytoskeletal integrity was compromised in patient cells, with decreases in alpha- and beta-dystroglycan (DAG1; 128239). The findings suggested disruption of protein homeostasis in fibroblasts and muscle. The authors observed an apparent genotype/phenotype correlation, with hypomorphic missense mutations resulting in a less severe phenotype and complete loss-of-function frameshift or nonsense mutations resulting in a more severe phenotype.

In 5 patients from 2 unrelated families with LGMDR29, Iruzubieta et al. (2024) identified a homozygous I309S mutation (607902.0001) in the SNUPN gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in both families. The variant was found at a low frequency in the gnomAD (v4.0) database (5.5 x 10(-6)). Patient blood samples and skin fibroblasts showed normal levels of SNUPN mRNA and protein, but there was abnormal cytoplasmic accumulation of U-snRNP proteins in fibroblasts and muscle samples. RNA-seq analysis of muscle samples from the patients in family 1 showed changes in expression of genes involved in muscle, neurons, collagen, and metabolic pathways, as well dysregulated splicing of muscle-related genes and spliceosome components. The findings suggested that the mutation likely causes functional impairment of SNUPN.

Iruzubieta et al. (2024) found that muscle-specific knockdown of snup (the ortholog of human SNUPN) in Drosophila caused a faster progression of age-dependent reduced climbing activity and decreased lifespan compared to controls.