Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond–like features
Raphael Carapito, et al.
Raphael Carapito, et al.
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Research Article Genetics Hematology

Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond–like features

Abstract

Shwachman-Diamond syndrome (SDS) (OMIM #260400) is a rare inherited bone marrow failure syndrome (IBMFS) that is primarily characterized by neutropenia and exocrine pancreatic insufficiency. Seventy-five to ninety percent of patients have compound heterozygous loss-of-function mutations in the Shwachman-Bodian-Diamond syndrome (sbds) gene. Using trio whole-exome sequencing (WES) in an sbds-negative SDS family and candidate gene sequencing in additional SBDS-negative SDS cases or molecularly undiagnosed IBMFS cases, we identified 3 independent patients, each of whom carried a de novo missense variant in srp54 (encoding signal recognition particle 54 kDa). These 3 patients shared congenital neutropenia linked with various other SDS phenotypes. 3D protein modeling revealed that the 3 variants affect highly conserved amino acids within the GTPase domain of the protein that are critical for GTP and receptor binding. Indeed, we observed that the GTPase activity of the mutated proteins was impaired. The level of SRP54 mRNA in the bone marrow was 3.6-fold lower in patients with SRP54-mutations than in healthy controls. Profound reductions in neutrophil counts and chemotaxis as well as a diminished exocrine pancreas size in a SRP54-knockdown zebrafish model faithfully recapitulated the human phenotype. In conclusion, autosomal dominant mutations in SRP54, a key member of the cotranslation protein-targeting pathway, lead to syndromic neutropenia with a Shwachman-Diamond–like phenotype.

Authors

Raphael Carapito, Martina Konantz, Catherine Paillard, Zhichao Miao, Angélique Pichot, Magalie S. Leduc, Yaping Yang, Katie L. Bergstrom, Donald H. Mahoney, Deborah L. Shardy, Ghada Alsaleh, Lydie Naegely, Aline Kolmer, Nicodème Paul, Antoine Hanauer, Véronique Rolli, Joëlle S. Müller, Elisa Alghisi, Loïc Sauteur, Cécile Macquin, Aurore Morlon, Consuelo Sebastia Sancho, Patrizia Amati-Bonneau, Vincent Procaccio, Anne-Laure Mosca-Boidron, Nathalie Marle, Naël Osmani, Olivier Lefebvre, Jacky G. Goetz, Sule Unal, Nurten A. Akarsu, Mirjana Radosavljevic, Marie-Pierre Chenard, Fanny Rialland, Audrey Grain, Marie-Christine Béné, Marion Eveillard, Marie Vincent, Julien Guy, Laurence Faivre, Christel Thauvin-Robinet, Julien Thevenon, Kasiani Myers, Mark D. Fleming, Akiko Shimamura, Elodie Bottollier-Lemallaz, Eric Westhof, Claudia Lengerke, Bertrand Isidor, Seiamak Bahram

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Figure 2

Structural impact of SRP54 mutations.

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Structural impact of SRP54 mutations. (A) Molecular model of the N and G...
(A) Molecular model of the N and G domains of SRP54 (PDB 2j37 chain W) and its SR (FtsY, PDB 1rj9 chain B). SRP54 and SR are in green and pink, respectively. The positions of SRP GTPase-specific motifs and the conserved nucleotide-binding elements (G1–G5) are indicated in orange and blue, respectively. The mutated residues are shown in red. Each partner binds a GTP molecule. (B) Close-up of the WT residue G226 and side-chain modeling of mutant E226. The very short distances between oxygens of E226 of SRP54 (dark red) and D43, T232, and G233 of the receptor (pink) induce repulsive electrostatic forces that perturb the stability of the complex. Assuming a given protein backbone fold, the observed distances of 1.9 to 2.5 Å are indeed lower than those of standard hydrogen bonds between a hydroxyl group and an oxygen atom (2.8 Å). (C) Close-up of the WT residue T115 and side-chain modeling of mutant A115. According to the model, the hydrogen bond between the hydroxyl side chain of T115 and GTP is lost when mutated to A115. This modification most likely impairs GTP binding. (D) Close-up of the WT and structural model of deletion in T117. As residues 115–117 are all threonine the deletion of threonine introduces an earlier start of the helix structure at G113. According to the structural model, residues 113–116 form extensive hydrogen bonds with GTP. The deletion of T117 may affect GTP binding through rearrangements of residues 113–116, but this is difficult to predict.