A comparative structural bioinformatics analysis of inherited mutations in β-D-Mannosidase across multiple species reveals a genotype-phenotype correlation

Abstract

BackgroundLysosomal β-D-mannosidase is a glycosyl hydrolase that breaks down the glycosidic bonds at the non-reducing end of N-linked glycoproteins. Hence, it is a crucial enzyme in polysaccharide degradation pathway. Mutations in the MANBA gene that codes for lysosomal β-mannosidase, result in improper coding and malfunctioning of protein, leading to β-mannosidosis. Studying the location of mutations on the enzyme structure is a rational approach in order to understand the functional consequences of these mutations. Accordingly, the pathology and clinical manifestations of the disease could be correlated to the genotypic modifications.ResultsThe wild-type and inherited mutations of β-mannosidase were studied across four different species, human, cow, goat and mouse employing a previously demonstrated comprehensive homology modeling and mutational mapping technique, which reveals a correlation between the variation of genotype and the severity of phenotype in β-mannosidosis. X-ray crystallographic structure of β-mannosidase from Bacteroides thetaiotaomicron was used as template for 3D structural modeling of the wild-type enzymes containing all the associated ligands. These wild-type models subsequently served as templates for building mutational structures. Truncations account for approximately 70% of the mutational cases. In general, the proximity of mutations to the active site determines the severity of phenotypic expressions. Mapping mutations to the MANBA gene sequence has identified five mutational hot-spots.ConclusionAlthough restrained by a limited dataset, our comprehensive study suggests a genotype-phenotype correlation in β-mannosidosis. A predictive approach for detecting likely β-mannosidosis is also demonstrated where we have extrapolated observed mutations from one species to homologous positions in other organisms based on the proximity of the mutations to the enzyme active site and their co-location from different organisms. Apart from aiding the detection of mutational hotspots in the gene, where novel mutations could be disease-implicated, this approach also provides a way to predict new disease mutations. Higher expression of the exoglycosidase chitobiase is said to play a vital role in determining disease phenotypes in human and mouse. A bigger dataset of inherited mutations as well as a parallel study of β-mannosidase and chitobiase activities in prospective patients would be interesting to better understand the underlying reasons for β-mannosidosis.

The structure of mammalian β‐mannosidase provides insight into β‐mannosidosis and nystagmus

“…In general, the nature of the mutation as well as its proximity to the active site may determine the severity of the phenotype observed . Thus, nonsense mutations Y126X, W192X, W231X, V321X, and Y485X leading to large truncations in β‐mannosidase typically show severe phenotypes .…”

Lysosomal storage disease in the brain: mutations of the β-mannosidase gene identified in autosomal dominant nystagmus

“…Patients with β-mannosidosis have a wide spectrum of neurological involvement, including intellectual disability, hearing loss, ataxia, and seizures. 13 Phenotypegenotype correlation analysis revealed that truncation mutations often cause severe phenotypes, whereas substitution mutations may show mild phenotypes (Supplementary Table S11 online). 13 This study extends the scope of β-mannosidosis to the autosomal-dominant inheritance of infantile nystagmus.…”

“…13 Phenotypegenotype correlation analysis revealed that truncation mutations often cause severe phenotypes, whereas substitution mutations may show mild phenotypes (Supplementary Table S11 online). 13 This study extends the scope of β-mannosidosis to the autosomal-dominant inheritance of infantile nystagmus. The heterozygous mutations in MANBA identified in this study may represent the least severe β-mannosidosis that is limited to the eye regulatory regions in brain.…”

“…Multiple sequence alignment of a region of human MANBA harboring the mutations with that of goats, cattle, and cats showed that both p.R638 and p.L749 are evolutionarily conserved in the four species, and β-mannosidosis has been previously reported in these species (Figure 2e Furthermore, structural bioinformatics analysis showed that the last domain from residue 572 to 879 (Figure 2e,f) stabilizes the β-mannosidase active sites (residues 342-571). 13 Because the positively charged arginine 638 was substituted by a slightly positive histidine, p.R638H may destabilize β-mannosidase by affecting the salt bridge D709 or the interaction between R641 and D709, as shown in a three-dimensional structural model (Figure 2f,g) that was established using PyMOL (L. Schrödinger, version 1.3r1; PDB ID code 2JE8). This assumption is supported by previous analysis of the p.R641H mutation, which caused β-mannosidosis deficiency.…”

Disorders of Glycoprotein Degradation

“…45 Neuropathology in Salers calves showed hydrocephalus and myelin deficiency in the cerebral hemispheres, cerebellum, and brainstem.…”