HGNC Approved Gene Symbol: SRP54
Cytogenetic location: 14q13.2 Genomic coordinates (GRCh38) : 14:34,982,992-35,029,567 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 14q13.2 | Neutropenia, severe congenital, 8, autosomal dominant | 618752 | Autosomal dominant | 3 |
SRP54, a component of the signal recognition particle (SRP), recognizes the signal peptide of secretory proteins and interacts with the signal recognition particle receptor (SRPR; 182180) to target the ribosome and the associated nascent chain to the endoplasmic reticulum (summary by Pool et al., 2002).
Patel and Austen (1996) isolated full-length human SRP54 from a placenta cDNA library. The 504-amino acid human SRP54 protein is identical to its canine ortholog. SRP54 orthologs are present in diverse organisms, including yeast, E. coli, and M. mycoides, with highest amino acid homology in the GTP-binding domain and significant similarity in the methionine-rich domain.
By screening a human hepatoma cDNA library with mouse Srp54 as probe, Gowda et al. (1997) isolated a full-length SRP54 cDNA. Human SRP54 protein differs at only 2 amino acids from the mouse protein.
By functional analysis, Gowda et al. (1997) showed that SRP54 binds to SRP RNA via the M-domain, but only in the presence of RNA-bound SRP19, and that it associates with the signal peptide of nascent polypeptide chains. RNA interaction requires the presence of a loop in the C-terminal M-domain. Signal peptide recognition most likely involves methionine-rich loops.
Using protein crosslinking, Pool et al. (2002) detected distinct modes in the binding of SRP to the ribosome. During signal peptide recognition, SRP54 is positioned at the exit site close to ribosomal proteins L23a (602326) and L35. When SRP54 contacts the signal recognition particle receptor (182180), SRP54 is rearranged such that it is no longer close to L23a. This repositioning may allow the translocon to dock with the ribosome, leading to insertion of the signal peptide into the translocation channel.
The signal recognition particle (SRP) is a ribonucleoprotein complex that mediates the targeting of proteins to the endoplasmic reticulum (ER). The complex consists of a 7S (or 7SL) RNA and 6 different proteins, SRP9 (600707), SRP14 (600708), SRP19 (182175), SRP54, SRP68 (604858), and SRP72 (602122). The proteins are bound to the 7S RNA as monomers (SRP19 and SRP54) or heterodimers (SRP9/SRP14 and SRP68/SRP72). SRP9 and SRP14 constitute the Alu domain of 7S, whereas the other 4 proteins belong to the S domain. SRP has at least 3 distinct functions that can be associated with the protein subunits: signal recognition, translational arrest, and ER membrane targeting by interaction with the docking protein (summary by Lingelbach et al., 1988).
For information on a signal recognition particle database, see Larsen et al. (1998).
Stumpf (2025) mapped the SRP54 gene to chromosome 14q13.2 based on an alignment of the SRP54 sequence (GenBank BC000652) with the genomic sequence (GRCh38).
Using site-directed mutagenesis, Huang et al. (2002) identified residues in human SRP54 required for binding to SRP RNA. SRP54 was present as a dimer in both solution crystal states, but only monomeric SRP54 bound SRP RNA. Molecular modeling revealed that SRP54 underwent a conformational change in the signal peptide-binding groove in response to SRP RNA. This conformational change allowed leu329, which is conserved as a nonpolar bulky residue across species, to position itself in closer proximity to the RNA-binding domain and become part of the hydrophobic core for SRP RNA binding.
Halic et al. (2004) presented the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, determined to 12-angstrom resolution by cryoelectron microscopy, enabled Halic et al. (2004) to generate a molecular model of SRP in its functional conformation. The model showed how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation factor-binding site of the ribosome, explaining its elongation arrest activity.
In 3 unrelated patients with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752) in whom mutations in the SBDS gene (607444) and other bone marrow failure syndrome genes were excluded, Carapito et al. (2017) identified de novo heterozygous mutations in the SRP54 gene (604857.0001-604857.0003). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, affected highly conserved residues in the GTPase domain and were predicted to affect GTP binding. The patients were identified from a cohort of over 84 patients with a similar phenotype who underwent genetic analysis or were ascertained through collaborative efforts. Patient bone marrow cells showed decreased levels of SRP54 mRNA, and the GTPase activity of the mutant proteins was variably reduced compared to controls. Morpholino knockdown of the srp54 gene in zebrafish resulted in similar phenotypic defects that were rescued by wildtype, but not mutant, SRP54. Carapito et al. (2017) postulated either haploinsufficiency or a dominant-negative molecular mechanism.
In 23 French patients with SCN8, including 16 patients with sporadic disease and 7 with familial disease, Bellanne-Chantelot et al. (2018) identified heterozygous mutations in the SRP54 gene (see, e.g, 604857.0001; 604857.0003; 604857.0004-604857.0006). The mutations, which occurred de novo in the sporadic cases, were all missense variants, except for a recurrent in-frame deletion of conserved residue thr117 (604857.0003), and all occurred in the GTPase domain. The mutations were initially found by whole-exome sequencing in 3 of 8 unrelated patients with sporadic disease (P11, P13, and P19) and in an affected father and daughter (family 14) out of 6 families with the disease. The mutations were confirmed by Sanger sequencing. The subsequent patients were identified from a second cohort of 66 French probands who underwent direct sequencing of the SRP54 gene. In vitro studies showed that patient granulocytes had decreased cellular proliferation, and increased apoptosis compared to controls, as well as evidence of ER stress and induction of autophagy. Knockdown of SRP54 using shRNA in a cell line resulted in similar abnormalities. The authors noted that both neutrophils and pancreatic exocrine cells are highly secretory, possibly rendering them more susceptible to defects in the SRP54 gene, which is involved in the maturation of secretory and membrane proteins.
Carapito et al. (2017) found that morpholino knockdown of the srp54 orthologs in zebrafish resulted in decreased number of basal neutrophils and impaired neutrophil migration and chemotaxis in response to injury compared to controls, as well as disturbed pancreatic development and exocrine pancreatic dysfunction. These defects could be rescued with wildtype SRP54.
In a 6-year-old boy (family A) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Carapito et al. (2017) identified a de novo heterozygous c.677G-A transition (c.677G-A, NM_003136.3) in the SRP54 gene, resulting in a gly226-to-glu (G226E) substitution at a highly conserved residue in the GTPase domain. The authors stated that the mutation occurred in exon 8. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the 1000 Genomes Project or ExAC databases, or in various other databases containing more than 100,000 exomes. Patient bone marrow cells showed decreased levels of SRP54 mRNA, and the GTPase activity of the mutant protein was reduced by a factor of 3.5 compared to controls. The patient also had neurodevelopmental delay and autism.
In a 1.5-year-old French boy (P22) with SCN8, Bellanne-Chantelot et al. (2018) identified a de novo heterozygous c.677G-A transition (c.677G-A, NM_003136.3) in the SRP54 gene, resulting in a G226E substitution. The authors stated that the mutation occurred in exon 9. The mutation was found by direct sequencing of the SRP54 gene. The patient also had neurodevelopmental delay and seizures.
In a 16-month-old girl (family B) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Carapito et al. (2017) identified a de novo heterozygous c.343A-G transition (c.343A-G, NM_003136.3) in the SRP54 gene, resulting in a thr115-to-ala (T115A) substitution at a highly conserved residue in the G1 region of the GTPase domain. The authors stated that the mutation occurred in exon 4. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the 1000 Genomes Project or ExAC databases, or in various other databases containing more than 100,000 exomes. Patient bone marrow cells showed decreased levels of SRP54 mRNA, and the GTPase activity of the mutant protein was almost completely abolished compared to controls.
In an 18-year-old man (family C) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Carapito et al. (2017) identified a de novo heterozygous 3-bp in-frame deletion (c.349_351del, NM_003136.3) in the SRP54 gene, resulting in the deletion of highly conserved residue thr117 (Thr117del) in the GTPase domain. The authors stated that the mutation occurred in exon 4. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the 1000 Genomes Project or ExAC databases, or in various other databases containing more than 100,000 exomes. In vitro studies showed that the GTPase activity of the mutant protein was moderately decreased by about 1.6-fold compared to controls.
Bellanne-Chantelot et al. (2018) identified a heterozygous Thr117del (c.349_351del, NM_003136.3) mutation in the SRP54 gene in 14 French patients with SCN8. The mutation occurred de novo in 7 patients and was inherited from an affected (2) or unaffected mosaic parent (1) in 3 cases; inheritance could not be determined in the 2 remaining cases. These authors stated that the mutation occurred in exon 5.
In an 8-year-old French boy (P1) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Bellanne-Chantelot et al. (2018) identified a de novo heterozygous c.337G-C transversion (c.337G-C, NM_003136.3) in exon 5 of the SRP54 gene, resulting in a gly113-to-arg (G113R) substitution at a highly conserved residue in the GTPase domain. The mutation was found by direct sequencing of the SRP54 gene.
In a 43-year-old French man (P21) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Bellanne-Chantelot et al. (2018) identified a de novo heterozygous c.668C-A transversion (c.668C-A, NM_003136.3) in exon 9 of the SRP54 gene, resulting in an ala223-to-asp (A223D) substitution at a highly conserved residue in the GTPase domain. The mutation was found by direct sequencing of the SRP54 gene. The patient also had neurodevelopmental delay and pancreatic lipomatosis.
In 25-year-old French man (P23) with autosomal dominant severe congenital neutropenia-8 (SCN8; 618752), Bellanne-Chantelot et al. (2018) identified a de novo heterozygous c.821G-A transition (c.821G-A, NM_003136.3) in exon 9 of the SRP54 gene, resulting in a gly274-to-asp (G274D) substitution at a highly conserved residue in the GTPase domain. The mutation was found by direct sequencing of the SRP54 gene. The patient also had neurodevelopmental delay and pancreatic lipomatosis.
Bellanne-Chantelot, C., Schmaltz-Panneau, B., Marty, C., Fenneteau, O., Callebaut, I., Clauin, S., Docet, A., Damaj, G.-L., Leblanc, T., Pellier, I., Stoven, C., Souquere, S., and 26 others. Mutations in the SRP54 gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome. Blood 132: 1318-1331, 2018. [PubMed: 29914977] [Full Text: https://doi.org/10.1182/blood-2017-12-820308]
Carapito, R., Konantz, M., Paillard, C., Miao, Z., Pichot, A., Leduc, M. S., Yang, Y., Bergstrom, K. L., Mahoney, D. H., Shardy, D. L., Alsaleh, G., Naegely, L., and 38 others. Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond-like features. J. Clin. Invest. 127: 4090-4103, 2017. [PubMed: 28972538] [Full Text: https://doi.org/10.1172/JCI92876]
Gowda, K., Chittenden, K., Zwieb, C. Binding site of the M-domain of human protein SRP54 determined by systematic site-directed mutagenesis of signal recognition particle RNA. Nucleic Acids Res. 25: 388-394, 1997. [PubMed: 9016569] [Full Text: https://doi.org/10.1093/nar/25.2.388]
Halic, M., Becker, T., Pool, M. R., Spahn, C. M. T., Grassucci, R. A., Frank, J., Beckmann, R. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427: 808-814, 2004. [PubMed: 14985753] [Full Text: https://doi.org/10.1038/nature02342]
Huang, Q., Abdulrahman, S., Yin, J., Zwieb, C. Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition. Biochemistry 41: 11362-11371, 2002. [PubMed: 12234178] [Full Text: https://doi.org/10.1021/bi025765t]
Larsen, N., Samuelsson, T., Swieb, C. The Signal Recognition Particle Database (SRPDB). Nucleic Acids Res. 26: 177-178, 1998. [PubMed: 9399828] [Full Text: https://doi.org/10.1093/nar/26.1.177]
Lingelbach, K., Zwieb, C., Webb, J., Marshallsay, C., Hoben, P., Walter, P., Dobberstein, B. Isolation and characterization of a cDNA clone encoding the 19 kDa protein of signal recognition particle (SRP): expression and binding to 7SL RNA. Nucleic Acids Res. 16: 9431-9442, 1988. [PubMed: 2460823] [Full Text: https://doi.org/10.1093/nar/16.20.9431]
Patel, S., Austen, B. Sequence of the highly conserved gene encoding the human 54kDa subunit of signal recognition particle. DNA Seq. 6: 167-170, 1996. [PubMed: 8722571] [Full Text: https://doi.org/10.3109/10425179609010204]
Pool, M. R., Stumm, J., Fulga, T. A., Sinning, I., Dobberstein, B. Distinct modes of signal recognition particle interaction with the ribosome. Science 297: 1345-1348, 2002. [PubMed: 12193787] [Full Text: https://doi.org/10.1126/science.1072366]
Stumpf, A. M. Personal Communication. Baltimore, Md. 1/16/2025.