Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations

Zhai, Lu; Feng, Lingling; Xia, Lin; Yin, Huiyong; Xiang, Song

doi:10.1038/ncomms11229

Cited by 37 publications

(52 citation statements)

References 62 publications

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“…31 Based on the observation that overexpression of GAA alone does not fully correct GSDIII, we sought to address the enzymatic deficiency, hallmark of the disease, by directly restoring the GDE enzyme activity with AAV vectors. The fact that GDE is a large cytosolic protein of 175 kDa with two different enzymatic domains 32 complicates the design of AAV vectors expressing the enzyme, and it does not allow for the development of gene therapy strategies based on cross-correction. 19,33,34 To overcome this limitation, we developed a dual AAV vector strategy 13,14,20,35 to express GDE transgene in liver and muscle.…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, amino acids 28-35 of the GAA pro-peptide were removed to generate a truncated version of the transgene. Transgene expression was under the control of the hepatocyte-specific human alpha-1 anti-trypsin (hAAT) promoter, combined with a synthetic human beta-globin-derived (HBB2) intron (32) and bovine growth hormone polyA (bGH). The entire expression cassette was flanked by the inverted terminal repeats of AAV serotype 2 for vector packaging.…”

Section: Human Gaa Transgene Engineering and Transgene Expression Casmentioning

confidence: 99%

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Rescue of GSDIII Phenotype with Gene Transfer Requires Liver- and Muscle-Targeted GDE Expression

et al. 2018

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Glycogen storage disease type III (GSDIII) is an autosomal recessive disorder caused by a deficiency of glycogen-debranching enzyme (GDE), which results in profound liver metabolism impairment and muscle weakness. To date, no cure is available for GSDIII and current treatments are mostly based on diet. Here we describe the development of a mouse model of GSDIII, which faithfully recapitulates the main features of the human condition. We used this model to develop and test novel therapies based on adeno-associated virus (AAV) vector-mediated gene transfer. First, we showed that overexpression of the lysosomal enzyme alpha-acid glucosidase (GAA) with an AAV vector led to a decrease in liver glycogen content but failed to reverse the disease phenotype. Using dual overlapping AAV vectors expressing the GDE transgene in muscle, we showed functional rescue with no impact on glucose metabolism. Liver expression of GDE, conversely, had a direct impact on blood glucose levels. These results provide proof of concept of correction of GSDIII with AAV vectors, and they indicate that restoration of the enzyme deficiency in muscle and liver is necessary to address both the metabolic and neuromuscular manifestations of the disease.

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Section: Discussionmentioning

confidence: 99%

Section: Human Gaa Transgene Engineering and Transgene Expression Casmentioning

confidence: 99%

Rescue of GSDIII Phenotype with Gene Transfer Requires Liver- and Muscle-Targeted GDE Expression

et al. 2018

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“…Hence, the altered conformation of the loop might affect the enzymatic activity of human GDE in case of the mutant protein. While Tyr1445 points into the active site of human GDE and corresponding residue in C. glabrata helps to hold the substrate in a proper position and orientation for hydrolysis (Zhai et al, ). Side chain conformation of Tyr1445 is maintained by hydrogen bonded interaction with Glu1502 in addition to hydrophobic interaction with side chains of Tyr1428, Trp1451, and Leu1503.…”

Section: Discussionmentioning

confidence: 99%

“…In order to comprehend the influence of novel missense variations on the structure and function of the GDE at the atomic detail, a three‐dimensional (3D) structure of the wild‐type and mutant proteins is required. Due to the absence of an experimentally determined structure of human GDE, its 3D model was built with the help of homology modeling program MODELLER 8.2 (Sali & Blundell, ; Shen & Sali, ) using crystal structure of its closest homologue Candida glabrata GDE (PDB: 5D06_A) (Zhai, Feng, Xia, Yin, & Xiang, ) as template. MODELLER builds the homology model of a protein of unknown 3D structure by satisfying the spatial restraints derived from the structure of homologous protein.…”

Section: Methodsmentioning

confidence: 99%

Spectrum of amyloglucosidase mutations in Asian Indian patients with Glycogen storage disease type III

Perveen

Gupta

Kumar

et al. 2020

American J of Med Genetics Pt A

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Glycogen storage disease type III (GSD III) is a rare autosomal recessive inborn error of glycogen degradation pathway due to deficiency or reduced activity of glycogen debranching enzyme (GDE) that results in accumulation of abnormal glycogen in the liver, muscle, and heart. The cardinal hallmarks are hepatomegaly, fasting hypoglycemia, seizures, growth retardation, progressive skeletal myopathy, and cardiomyopathy in few. To date, 258 mutations in amyloglucosidase (AGL) gene have been identified worldwide. However, the mutation spectrum in the Asian Indian region is yet to be well characterized. We investigated 24 patients of Asian origin from 21 unrelated families with a provisional diagnosis of GSD III based on clinical and biochemical criteria. Molecular diagnosis was assessed by bidirectional sequencing and the impact of novel missense variants on the tertiary (three-dimensional) structure of GDE was evaluated by molecular modeling approach. Eighteen different pathogenic variants were identified, out of which 78% were novel. Novel variants included five nonsense, three small duplications and two small deletions, a splice site variant, and three missense variants. Variations in Exons 4, 14, 19, 24, 27, and 33 accounted for 61% of the total pathogenic variants identified and Allele p.Gly798Alafs*3 showed a high allele frequency of 11%. Molecular modeling study of novel pathogenic missense variants indicated the probable underlying molecular mechanism of adverse impact of variations on the structure and catalytic function of human GDE. Our study is the first large study on GSD III from the Asian subcontinent, which further expands the mutation spectrum of AGL.

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“…For instance, patatin-like phospholipase domain-containing protein 2 involves in energy homeostasis and storage through lipolysis (Yang & Mottillo, 2020). Glycogen debranching enzyme plays role in glycogen breakdown (Zhai et al, 2016). Phosphoenolpyruvate carboxykinase plays role in phosphoenolpyruvate synthesis for gluconeogenesis (Yang, Kalhan & Hanson, 2009).…”

Section: Transcriptomic Profiling In Shrimp Intestines Under Differenmentioning

confidence: 99%

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance

Uengwetwanit

Uawisetwathana

Arayamethakorn

et al. 2020

PeerJ

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Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal’s growth performance. Here, we compared the bacterial profiles along with the shrimp’s gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might contribute to different degrees of shrimp growth performance. A non-targeted metabolome analysis from shrimp intestines revealed different metabolic responsive patterns, in which the Top-weight shrimp contained significantly higher levels of short chain fatty acids, lipids and organic compounds than the Bottom-weight shrimp. The identified metabolites included those that were known to be produced by intestinal bacteria such as butyric acid, 4-indolecarbaldehyde and L-3-phenyllactic acid as well as those produced by shrimp such as acyl-carnitines and lysophosphatidylcholine. The functions of these metabolites were related to nutrient absorption and metabolisms. Our findings provide the first report utilizing multi-omics integration approach to investigate microbiota, metabolic and transcriptomics profiles of the host shrimp and their potential roles and relationship to shrimp growth performance.

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Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations

Cited by 37 publications

References 62 publications

Rescue of GSDIII Phenotype with Gene Transfer Requires Liver- and Muscle-Targeted GDE Expression

Rescue of GSDIII Phenotype with Gene Transfer Requires Liver- and Muscle-Targeted GDE Expression

Spectrum of amyloglucosidase mutations in Asian Indian patients with Glycogen storage disease type III

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance

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