scholarly journals Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability

2019 ◽  
Vol 116 (30) ◽  
pp. 14961-14970 ◽  
Author(s):  
Veronica M. Pravata ◽  
Villo Muha ◽  
Mehmet Gundogdu ◽  
Andrew T. Ferenbach ◽  
Poonam S. Kakade ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Catalytic Domain ◽  
Embryonic Stem ◽  
Global Changes ◽  
Missense Mutations ◽  
Protein Protein Interactions ◽  
Delayed Differentiation ◽  
Nucleocytoplasmic Proteins ◽  
Glcnac Transferase

O-GlcNAc transferase (OGT) is an X-linked gene product that is essential for normal development of the vertebrate embryo. It catalyses the O-GlcNAc posttranslational modification of nucleocytoplasmic proteins and proteolytic maturation of the transcriptional coregulator Host cell factor 1 (HCF1). Recent studies have suggested that conservative missense mutations distal to the OGT catalytic domain lead to X-linked intellectual disability in boys, but it is not clear if this is through changes in the O-GlcNAc proteome, loss of protein–protein interactions, or misprocessing of HCF1. Here, we report an OGT catalytic domain missense mutation in monozygotic female twins (c. X:70779215 T > A, p. N567K) with intellectual disability that allows dissection of these effects. The patients show limited IQ with developmental delay and skewed X-inactivation. Molecular analyses revealed decreased OGT stability and disruption of the substrate binding site, resulting in loss of catalytic activity. Editing this mutation into the Drosophila genome results in global changes in the O-GlcNAc proteome, while in mouse embryonic stem cells it leads to loss of O-GlcNAcase and delayed differentiation down the neuronal lineage. These data imply that catalytic deficiency of OGT could contribute to X-linked intellectual disability.

scholarly journals Dual functionality of O -GlcNAc transferase is required for Drosophila development

Open Biology ◽  
2015 ◽  
Vol 5 (12) ◽  
pp. 150234 ◽  
Author(s):  
Daniel Mariappa ◽  
Xiaowei Zheng ◽  
Marianne Schimpl ◽  
Olawale Raimi ◽  
Andrew T. Ferenbach ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rational Design ◽  
Catalytic Domain ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Tetratricopeptide Repeats ◽  
Sex Combs ◽  
Glcnac Transferase ◽  
Activity Dependent

Post-translational modification of intracellular proteins with O -linked N -acetylglucosamine ( O -GlcNAc) catalysed by O -GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein–protein interactions. Drosophila OGT ( Dm OGT) is encoded by super sex combs ( sxc ), mutants of which are pupal lethal. However, it is not clear if this phenotype is caused by reduction of O -GlcNAcylation. Here we use a genetic approach to demonstrate that post-pupal Drosophila development can proceed with negligible OGT catalysis, while early embryonic development is OGT activity-dependent. Structural and enzymatic comparison between human OGT (hOGT) and Dm OGT informed the rational design of Dm OGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements sxc pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of Hox genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.

scholarly journals Generation of an Unbiased Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability

2020 ◽  
Author(s):  
Hannah M Stephen ◽  
Jeremy L Praissman ◽  
Lance Wells
Keyword(s):  
Intellectual Disability ◽  
Missense Mutations ◽  
Substantial Impact ◽  
Cellular Survival ◽  
Cellular Processes ◽  
Disease States ◽  
Tetratricopeptide Repeat Domain ◽  
Nucleocytoplasmic Proteins ◽  
Glcnac Transferase ◽  
Tpr Domain

The O-GlcNActransferase (OGT) is localized to the nucleus and cytoplasm where it regulates nucleocytoplasmic proteins by modifying serine and threonine residues with a non-extended monosaccharide, b-N-Acetyl-Glucosamine (O-GlcNAc). With thousands ofknown O-GlcNAcmodifiedproteinsbut only oneOGTencoded in the mammalian genome, a prevailing question is howOGTselects its substrates. Prior work has indicated that theN-terminaltetratricopeptide repeat (TPR) domain of OGT, rather than itsC-terminalcatalytic domain, is responsible forsubcellular targeting andsubstrate selection.An additional impetus for exploring the OGT TPR domain interactome is the fact that missense mutations inOGTassociated with X-linked intellectual disability (XLID) are primarily localized to the TPR domain without substantial impact on activity or stability of the enzyme.Therefore, we adapted theBioIDlabeling method to identify interactors of a TPR-BirA* fusion protein in HeLa cells. We identified 115high confidenceinteractors representing both known and novel O-GlcNAcmodified proteins and OGT interactors. The TPR interactors are highly enriched in processes in which OGT has a known role (e.g. chromatin remodeling, cellular survival of heat stress, circadian rhythm), as well as processesin which OGT has yet to be implicated (e.g. pre-mRNA processing). Importantly,the identified TPR interactors are involved in several disease states but most notably are highly enriched in pathologies featuring intellectual disability.Theseproteinsrepresent candidateinteractors that may underlie the mechanismby which mutations in OGT lead to XLID. Furthermore, the identified interactors provide additional evidence of the importance of the TPR domain for OGT targeting and/or substrate selection.Thus, this defined interactome for the TPR domain of OGT serves as ajumping off point for future researchexploringthe role of OGT, the TPR domain, and its protein interactorsin multiple cellular processes and disease mechanisms, including intellectual disability.

Swim-exercised mice show a decreased level of protein O-GlcNAcylation and expression of O-GlcNAc transferase in heart

2011 ◽  
Vol 111 (1) ◽  
pp. 157-162 ◽  
Author(s):  
Darrell D. Belke
Keyword(s):  
Protein Interactions ◽  
Contractile Function ◽  
Cell Physiology ◽  
Protein Protein Interactions ◽  
Training Exercise ◽  
General Protein ◽  
Exercise Induced ◽  
Glcnac Transferase ◽  
The Impact ◽  
Physiological Hypertrophy

Swim-training exercise in mice leads to cardiac remodeling associated with an improvement in contractile function. Protein O-linked N-acetylglucosamine ( O-GlcNAcylation) is a posttranslational modification of serine and threonine residues capable of altering protein-protein interactions affecting gene transcription, cell signaling pathways, and general cell physiology. Increased levels of protein O-GlcNAcylation in the heart have been associated with pathological conditions such as diabetes, ischemia, and hypertrophic heart failure. In contrast, the impact of physiological exercise on protein O-GlcNAcylation in the heart is currently unknown. Swim-training exercise in mice was associated with the development of a physiological hypertrophy characterized by an improvement in contractile function relative to sedentary mice. General protein O-GlcNAcylation was significantly decreased in swim-exercised mice. This effect was mirrored in the level of O-GlcNAcylation of individual proteins such as SP1. The decrease in protein O-GlcNAcylation was associated with a decrease in the expression of O-GlcNAc transferase (OGT) and glutamine-fructose amidotransferase (GFAT) 2 mRNA. O-GlcNAcase (OGA) activity was actually lower in swim-trained than sedentary hearts, suggesting that it did not contribute to the decreased protein O-GlcNAcylation. Thus it appears that exercise-induced physiological hypertrophy is associated with a decrease in protein O-GlcNAcylation, which could potentially contribute to changes in gene expression and other physiological changes associated with exercise.

scholarly journals mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

2019 ◽  
Vol 47 (W1) ◽  
pp. W338-W344 ◽  
Author(s):  
Carlos H M Rodrigues ◽  
Yoochan Myung ◽  
Douglas E V Pires ◽  
David B Ascher
Keyword(s):  
Protein Interactions ◽  
Interaction Network ◽  
Evolutionary Information ◽  
Biological Processes ◽  
Missense Mutations ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Residue Interaction ◽  
User Friendly ◽  
Network Metrics

AbstractProtein–protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predict the effects of missense mutations on protein–protein interaction binding affinity. mCSM-PPI2 uses graph-based structural signatures to model effects of variations on the inter-residue interaction network, evolutionary information, complex network metrics and energetic terms to generate an optimised predictor. We demonstrate that our method outperforms previous methods, ranking first among 26 others on CAPRI blind tests. mCSM-PPI2 is freely available as a user friendly webserver at http://biosig.unimelb.edu.au/mcsm_ppi2/.

scholarly journals Crystal Structure of SEDL and Its Implications for a Genetic Disease Spondyloepiphyseal Dysplasia Tarda

2002 ◽  
Vol 277 (51) ◽  
pp. 49863-49869 ◽  
Author(s):  
Se Bok Jang ◽  
Yeon-Gil Kim ◽  
Yong-Soon Cho ◽  
Pann-Ghill Suh ◽  
Kyung-Hwa Kim ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Genetic Disease ◽  
Point Mutations ◽  
Missense Mutations ◽  
Protein Protein Interactions ◽  
Spondyloepiphyseal Dysplasia ◽  
Multiple Protein ◽  
Protein Particle ◽  
Eukaryotic Organisms ◽  
Spondyloepiphyseal Dysplasia Tarda

SEDL is an evolutionarily highly conserved protein in eukaryotic organisms. Deletions or point mutations in theSEDLgene are responsible for the genetic disease spondyloepiphyseal dysplasia tarda (SEDT), an X-linked skeletal disorder. SEDL has been identified as a component of the transport protein particle (TRAPP), critically involved in endoplasmic reticulum-to-Golgi vesicle transport. Herein, we report the 2.4 Å resolution structure of SEDL, which reveals an unexpected similarity to the structures of the N-terminal regulatory domain of two SNAREs, Ykt6p and Sec22b, despite no sequence homology to these proteins. The similarity and the presence of unusually many solvent-exposed apolar residues of SEDL suggest that it serves regulatory and/or adaptor functions through multiple protein-protein interactions. Of the four known missense mutations responsible for SEDT, three mutations (S73L, F83S, V130D) map to the protein interior, where the mutations would disrupt the structure, and the fourth (D47Y) on a surface at which the mutation may abrogate functional interactions with a partner protein.

scholarly journals Structure of PDE3A–SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jie Chen ◽  
Nan Liu ◽  
Yinpin Huang ◽  
Yuanxun Wang ◽  
Yuxing Sun ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Catalytic Domain ◽  
Cultured Cells ◽  
Hydrophobic Interactions ◽  
Complex Structure ◽  
Protein A ◽  
Protein Translation ◽  
Protein Protein Interactions ◽  
Cryo Electron Microscopy ◽  
Apoptosis Inducer

AbstractMolecular glues are a class of small molecular drugs that mediate protein-protein interactions, that induce either the degradation or stabilization of target protein. A structurally diverse group of chemicals, including 17-β-estradiol (E2), anagrelide, nauclefine, and DNMDP, induces apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (SLFN12). They do so by binding to the PDE3A enzymatic pocket that allows the compound-bound PDE3A to recruit and stabilize SLFN12, which in turn blocks protein translation, leading to apoptosis. In this work, we report the high-resolution cryo-electron microscopy structure of PDE3A-SLFN12 complexes isolated from cultured HeLa cells pre-treated with either anagrelide, or nauclefine, or DNMDP. The PDE3A-SLFN12 complexes exhibit a butterfly-like shape, forming a heterotetramer with these small molecules, which are packed in a shallow pocket in the catalytic domain of PDE3A. The resulting small molecule-modified interface binds to the short helix (E552-I558) of SLFN12 through hydrophobic interactions, thus “gluing” the two proteins together. Based on the complex structure, we designed and synthesized analogs of anagrelide, a known drug used for the treatment of thrombocytosis, to enhance their interactions with SLFN12, and achieved superior efficacy in inducing apoptosis in cultured cells as well as in tumor xenografts.

scholarly journals A missense mutation in the catalytic domain of O ‐GlcNAc transferase links perturbations in protein O ‐GlcNAcylation to X‐linked intellectual disability

FEBS Letters ◽  
2019 ◽  
Vol 594 (4) ◽  
pp. 717-727 ◽  
Author(s):  
Veronica M. Pravata ◽  
Mehmet Gundogdu ◽  
Sergio G. Bartual ◽  
Andrew T. Ferenbach ◽  
Marios Stavridis ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Missense Mutation ◽  
Catalytic Domain ◽  
Glcnac Transferase

scholarly journals Molecular basis for the interaction between human choline kinase alpha and the SH3 domain of the c-Src tyrosine kinase

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefanie L. Kall ◽  
Kindra Whitlatch ◽  
Thomas E. Smithgall ◽  
Arnon Lavie
Keyword(s):  
Crystal Structures ◽  
Protein Interactions ◽  
Catalytic Domain ◽  
Sh3 Domain ◽  
Crystallographic Analysis ◽  
Choline Kinase ◽  
Protein Protein Interactions ◽  
Src Tyrosine Kinase ◽  
Patient Prognosis ◽  
Co Precipitation

AbstractCholine kinase alpha is a 457-residue protein that catalyzes the reaction between ATP and choline to yield ADP and phosphocholine. This metabolic action has been well studied because of choline kinase’s link to cancer malignancy and poor patient prognosis. As the myriad of x-ray crystal structures available for this enzyme show, chemotherapeutic drug design has centered on stopping the catalytic activity of choline kinase and reducing the downstream metabolites it produces. Furthermore, these crystal structures only reveal the catalytic domain of the protein, residues 80–457. However, recent studies provide evidence for a non-catalytic protein-binding role for choline kinase alpha. Here, we show that choline kinase alpha interacts with the SH3 domain of c-Src. Co-precipitation assays, surface plasmon resonance, and crystallographic analysis of a 1.5 Å structure demonstrate that this interaction is specific and is mediated by the poly-proline region found N-terminal to the catalytic domain of choline kinase. Taken together, these data offer strong evidence that choline kinase alpha has a heretofore underappreciated role in protein-protein interactions, which offers an exciting new way to approach drug development against this cancer-enhancing protein.

scholarly journals Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31

2020 ◽  
Vol 9 (1) ◽  
pp. 274
Author(s):  
Jonathan D. J. Labonne ◽  
Terri M. Driessen ◽  
Marvin E. Harris ◽  
Il-Keun Kong ◽  
Soumia Brakta ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Human Brain ◽  
Protein Interactions ◽  
Genomic Mapping ◽  
Comparative Genomic ◽  
Protein Protein Interactions ◽  
Binding Partners ◽  
Expression Studies ◽  
Affected Member ◽  
Chromosome Regions

We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.

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