| Literature DB >> 26834553 |
Philip Long1, Melanie M May2, Victoria M James1, Simone Grannò1, John P Johnson3, Patrick Tarpey4, Roger E Stevenson2, Kirsten Harvey1, Charles E Schwartz2, Robert J Harvey1.
Abstract
Non-syndromal X-linked intellectual disability (NS-XLID) represents a broad group of clinical disorders in which ID is the only clinically consistent manifestation. Although in many cases either chromosomal linkage data or knowledge of the >100 existing XLID genes has assisted mutation discovery, the underlying cause of disease remains unresolved in many families. We report the resolution of a large family (K8010) with NS-XLID, with variable macrocephaly and macro-orchidism. Although a previous linkage study had mapped the locus to Xq12-q21, this region contained too many candidate genes to be analyzed using conventional approaches. However, X-chromosome exome sequencing, bioinformatics analysis and segregation analysis revealed a novel missense mutation (c.1012C>T; p.R338W) in ARHGEF9. This gene encodes collybistin (CB), a neuronal GDP-GTP exchange factor previously implicated in several cases of XLID, as well as clustering of gephyrin and GABAA receptors at inhibitory synapses. Molecular modeling of the CB R338W substitution revealed that this change results in the substitution of a long electropositive side-chain with a large non-charged hydrophobic side-chain. The R338W change is predicted to result in clashes with adjacent amino acids (K363 and N335) and disruption of electrostatic potential and local folding of the PH domain, which is known to bind phosphatidylinositol-3-phosphate (PI3P/PtdIns-3-P). Consistent with this finding, functional assays revealed that recombinant CB CB2SH3- (R338W) was deficient in PI3P binding and was not able to translocate EGFP-gephyrin to submembrane microaggregates in an in vitro clustering assay. Taken together, these results suggest that the R338W mutation in ARHGEF9 is the underlying cause of NS-XLID in this family.Entities:
Keywords: ARHGEF9; PH domain; XLID; collybistin; gephyrin
Year: 2016 PMID: 26834553 PMCID: PMC4719118 DOI: 10.3389/fnmol.2015.00083
Source DB: PubMed Journal: Front Mol Neurosci ISSN: 1662-5099 Impact factor: 5.639
Figure 1Identification of a R338W mutation in Pedigree of the K8010 family, which has been updated. Open symbols represent normal individuals, filled squares represent affected males. Individuals tested for the nucleotide substitution in each family are indicated with either a T (mutant allele) or a C (normal allele). (B) DNA sequence electropherograms for the c.1012C>T mutation reported in this study. (C) Schematic of the human collybistin (CB) protein with a regulatory SH3 domain, a catalytic RhoGEF domain and a pleckstrin homology (PH) domain. The relative locations of known missense and nonsense mutations in ARHGEF9 are shown. (D) Sequence alignments of CB proteins from various species showing the high conservation of R338W in the PH domain. Note that R338W is not one of the known PI3P binding residues (R356 and R357, green).
Figure 2The R338W substitution is predicted to influence the electrostatic potential and folding of the CB PH domain. (A) Arginine 338 is located on the surface of the CB structure within the pleckstrin homology (PH) domain (circled by a black dotted line). It resides within a cleft between turns of β-sheet secondary structure (D), in close proximity to other electropositive side-chains. Therefore, an area of hydrophobicity is created (B) close to the polar heads of the cell membrane. It is predicted that substitution of arginine with tryptophan at position 338 changes the hydrophobicity of this area, making it neutral in charge (C). In addition, the bulky side-chain of tryptophan introduces clashes with surrounding side chains of lysine 363 and asparagine 335 (E), disrupting the overall structure of the protein in this region.
Figure 3R338W reduces collybistin PI Human embryonic kidney (HEK293) cells were transfected with plasmids encoding myc-CB3SH3− or myc-CB3SH3−R338W and cell lysates incubated with PI3P-conjugated agarose beads. After washing, bound material was subjected to SDS-PAGE and analyzed by immunoblotting with an anti-myc antibody (Sigma). Notably, no significant difference was observed in total level of myc-CB3SH3−R338W expression in comparison with wild-type CB3SH3−, using β-actin as a loading control (A, left and right panels, normalized to wild-type 1.00 ± 0.23 vs. R338W 1.16 ± 0.33; wild-type ± SEM, n = 5). myc-CB3SH3−R338W binding to PI3P was significantly reduced (62.7% ± 3.9%) in comparison to wild-type CB3SH3−. When we assessed the PI3P pull-down fraction as a percentage of the raw input, we saw a significant difference between wild-type and the R338W variant (A, middle and right panels; wild-type 100 ± 13.5 vs. R338W 38 ± 8.6; pull-down fraction ± SEM, n = 5, **p < 0.006, unpaired student’s t-test). No β-actin immunoreactivity was observed in PI3P pull-down samples, confirming the validity of this assay. (B–G) HEK293 cells were co-transfected with EGFP-gephyrin alone (B), or with myc-CB3SH3− (C), myc-CB3SH3+ (D), myc-CB3SH3−R338W (E), or the PI3P binding defective mutants myc-CB3SH3−R290H (F), and myc-CB3SH3−R356N/R357N (G). Cells were immunostained using anti-myc and AlexaFluor 546 antibodies and co-stained with a nuclear marker (DAPI). Note that while myc-CB3SH3− co-localizes with gephyrin in submembrane clusters, all other CB variants co-localize with gephyrin in large intracellular aggregates, consistent with a lack of CB-mediated gephyrin clustering activity. Scale bar = 10 μm. (C) is a Z-projection, all other images are single plane.
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| Mutation type | Nucleotide | Protein | Reported phenotype | Reference |
|---|---|---|---|---|
| Missense and nonsense mutations | c.4C>T | p.Q2X | Refractory seizures, right frontal polymicrogyria, severe psychomotor retardation, ataxia | Shimojima et al. ( |
| c.869G>A | p.G55A | Hyperekplexia, early infantile epileptic encephalopathy and severe psychomotor retardation | Harvey et al. ( | |
| c.869G>A | p.R290H | Epilepsy and intellectual disability | Lemke et al. ( | |
| c.1012C>T | p.R338W | Intellectual disability with variable macrocephaly and macro-orchidism | This study | |
| Deletions | Complex partial seizures, severely delayed psychomotor development, generalized overgrowth and trigonocephaly | Kalscheuer et al. ( | ||
| Delayed psychomotor development, loss of consciousness, hypotonia, cyanosis, generalized overgrowth, mild dysmorphic features, hyperactivity with attention deficit, limited social interaction | Marco et al. ( | |||
| Complex rearrangements | Balanced translocation 46, X, t(Xq11.1;18q11.21) | Disturbed sleep-wake cycle, late-onset epileptic seizures, increased anxiety, aggressive behavior and intellectual disability | Kalscheuer et al. ( | |
| Balanced | Hyperarousal (noise and social situations), global developmental delay, dysarthric speech, difficulty with smooth eye pursuit, bilateral lower extremity spasticity, brisk reflexes and extensor plantar responses, wide-based gait | Marco et al. ( | ||