scholarly journals A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy

2021 ◽  
Author(s):  
Min Ni ◽  
Bushra Afroze ◽  
Chao Xing ◽  
Chunxiao Pan ◽  
Yanqiu Shao ◽  
...  
Keyword(s):  
Protein Modification ◽  
Catalytic Domain ◽  
Gene Encoding ◽  
Post Translational Modifications ◽  
Neurodevelopmental Delay ◽  
Pathogenic Variants ◽  
Recessive Form ◽  
Clinical Consequences ◽  
Regions Of Homozygosity ◽  
Conserved Residue

Abstract Purpose Neurodevelopmental disabilities are common and genetically heterogeneous. We identified a homozygous variant in the gene encoding UFM1-specific peptidase 2 (UFSP2), which participates in the UFMylation pathway of protein modification. UFSP2 variants are implicated in autosomal dominant skeletal dysplasias, but not neurodevelopmental disorders. Homozygosity for the variant occurred in eight children from four South Asian families with neurodevelopmental delay and epilepsy. We describe the clinical consequences of this variant and its effect on UFMylation. Methods Exome sequencing was used to detect potentially pathogenic variants and identify shared regions of homozygosity. Immunoblotting assessed protein expression and post-translational modifications in patient-derived fibroblasts. Results The variant (c.344T>A; p.V115E) is rare and alters a conserved residue in UFSP2. Immunoblotting in patient-derived fibroblasts revealed reduced UFSP2 abundance and increased abundance of UFMylated targets, indicating the variant may impair de-UFMylation rather than UFMylation. Reconstituting patient-derived fibroblasts with wild-type UFSP2 reduced UFMylation marks. Analysis of UFSP2’s structure indicated that variants observed in skeletal disorders localize to the catalytic domain, whereas V115 resides in an N-terminal domain possibly involved in substrate binding. Conclusion Different UFSP2 variants cause markedly different diseases, with homozygosity for V115E causing a severe syndrome of neurodevelopmental disability and epilepsy.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

The Involvement of Post-Translational Modifications in Alzheimer's Disease

2018 ◽  
Vol 15 (4) ◽  
pp. 313-335 ◽  
Author(s):  
Serena Marcelli ◽  
Massimo Corbo ◽  
Filomena Iannuzzi ◽  
Lucia Negri ◽  
Fabio Blandini ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Modification ◽  
Neurodegenerative Disorder ◽  
Amyloid Β ◽  
Normal Function ◽  
Ageing Population ◽  
Covalent Bonds ◽  
Post Translational Modifications ◽  
Related Proteins

Background: Alzheimer's disease (AD) is a neurodegenerative disorder recognized as the most common cause of chronic dementia among the ageing population. AD is histopathologically characterized by progressive loss of neurons and deposits of insoluble proteins, primarily composed of amyloid-β pelaques and neurofibrillary tangles (NFTs). Methods: Several molecular processes contribute to the formation of AD cellular hallmarks. Among them, post-translational modifications (PTMs) represent an attractive mechanism underlying the formation of covalent bonds between chemical groups/peptides to target proteins, which ultimately result modified in their function. Most of the proteins related to AD undergo PTMs. Several recent studies show that AD-related proteins like APP, Aβ, tau, BACE1 undergo post-translational modifications. The effect of PTMs contributes to the normal function of cells, although aberrant protein modification, which may depend on many factors, can drive the onset or support the development of AD. Results: Here we will discuss the effect of several PTMs on the functionality of AD-related proteins potentially contributing to the development of AD pathology. Conclusion: We will consider the role of Ubiquitination, Phosphorylation, SUMOylation, Acetylation and Nitrosylation on specific AD-related proteins and, more interestingly, the possible interactions that may occur between such different PTMs.

scholarly journals Two Monogenetic Disorders, Activated PI3-Kinase-δ Syndrome 2 and Smith–Magenis Syndrome, in One Patient: Case Report and a Literature Review of Neurodevelopmental Impact in Primary Immunodeficiencies Associated With Disturbed PI3K Signaling

2021 ◽  
Vol 9 ◽  
Author(s):  
Nidia Moreno-Corona ◽  
Loïc Chentout ◽  
Lucie Poggi ◽  
Romane Thouenon ◽  
Cecile Masson ◽  
...  
Keyword(s):  
Viral Infections ◽  
Genetic Disorder ◽  
Pi3 Kinase ◽  
Pi3k Signaling ◽  
Gene Encoding ◽  
Regulatory Subunits ◽  
Neurodevelopmental Delay ◽  
Exon 11 ◽  
Complex Genetic Disorder ◽  
Splice Product

Activated PI3-kinase-δ syndrome 2 (APDS2) is caused by autosomal dominant mutations in the PIK3R1 gene encoding the p85α, p55α, and p50α regulatory subunits. Most diagnosed APDS2 patients carry mutations affecting either the splice donor or splice acceptor sites of exon 11 of the PIK3R1 gene responsible for an alternative splice product and a shortened protein. The clinical presentation of APDS2 patients is highly variable, ranging from mild to profound combined immunodeficiency features as massive lymphoproliferation, increased susceptibility to bacterial and viral infections, bronchiectasis, autoimmune manifestations, and occurrence of cancer. Non-immunological features such as growth retardation and neurodevelopmental delay have been reported for APDS2 patients. Here, we describe a patient suffering from an APDS2 associated with a Smith–Magenis syndrome (SMS), a complex genetic disorder affecting, among others, neurological manifestations and review the literature describing neurodevelopmental impacts in APDS2 and other PIDs/monogenetic disorders associated with dysregulated PI3K signaling.

Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts

2018 ◽  
Vol 55 (11) ◽  
pp. 753-764 ◽  
Author(s):  
Miroslav P Milev ◽  
Claudio Graziano ◽  
Daniela Karall ◽  
Willemijn F E Kuper ◽  
Noraldin Al-Deri ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Membrane Trafficking ◽  
Neurodevelopmental Disorder ◽  
Febrile Illness ◽  
Missense Variant ◽  
Energy Status ◽  
Protein Protein Interactions ◽  
Neurodevelopmental Delay ◽  
Pathogenic Variants ◽  
Similar Phenotype

BackgroundThe combination of febrile illness-induced encephalopathy and rhabdomyolysis has thus far only been described in disorders that affect cellular energy status. In the absence of specific metabolic abnormalities, diagnosis can be challenging.ObjectiveThe objective of this study was to identify and characterise pathogenic variants in two individuals from unrelated families, both of whom presented clinically with a similar phenotype that included neurodevelopmental delay, febrile illness-induced encephalopathy and episodes of rhabdomyolysis, followed by developmental arrest, epilepsy and tetraplegia.MethodsWhole exome sequencing was used to identify pathogenic variants in the two individuals. Biochemical and cell biological analyses were performed on fibroblasts from these individuals and a yeast two-hybrid analysis was used to assess protein-protein interactions.ResultsProbands shared a homozygous TRAPPC2L variant (c.109G>T) resulting in a p.Asp37Tyr missense variant. TRAPPC2L is a component of transport protein particle (TRAPP), a group of multisubunit complexes that function in membrane traffic and autophagy. Studies in patient fibroblasts as well as in a yeast system showed that the p.Asp37Tyr protein was present but not functional and resulted in specific membrane trafficking delays. The human missense mutation and the analogous mutation in the yeast homologue Tca17 ablated the interaction between TRAPPC2L and TRAPPC10/Trs130, a component of the TRAPP II complex. Since TRAPP II activates the GTPase RAB11, we examined the activation state of this protein and found increased levels of the active RAB, correlating with changes in its cellular morphology.ConclusionsOur study implicates a RAB11 pathway in the aetiology of the TRAPPC2L disorder and has implications for other TRAPP-related disorders with similar phenotypes.

scholarly journals Ten novel insertion/deletion variants in MECP2 identified in Japanese patients with Rett syndrome

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Eri Takeshita ◽  
Aritoshi Iida ◽  
Chihiro Abe-Hatano ◽  
Eiji Nakagawa ◽  
Masayuki Sasaki ◽  
...  
Keyword(s):  
Rett Syndrome ◽  
Neurological Disorder ◽  
Binding Protein ◽  
Japanese Patients ◽  
Gene Encoding ◽  
Pathogenic Variants

Abstract Rett syndrome (RTT) is an X-linked progressive and severe neurological disorder caused by mutations in the gene encoding methyl CpG binding protein 2 (MECP2). Among the 49 typical RTT patients examined, we identified 10 novel and eight known insertion/deletion variants, and 31 known pathogenic variants in MECP2. The pathogenic variants presented here should be a useful resource for examining the correlation between the genotypes and phenotypes of RTT.

The new world of inorganic polyphosphates

2016 ◽  
Vol 44 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Cristina Azevedo ◽  
Adolfo Saiardi
Keyword(s):  
Protein Modification ◽  
Biochemical Characterization ◽  
Covalent Attachment ◽  
Detection Methods ◽  
Inorganic Polyphosphate ◽  
Post Translational Modifications ◽  
Topoisomerase 1 ◽  
Lysine Residues ◽  
Acidic Conditions

Post-translational modifications (PTMs) add regulatory features to proteins that help establish the complex functional networks that make up higher organisms. Advances in analytical detection methods have led to the identification of more than 200 types of PTMs. However, some modifications are unstable under the present detection methods, anticipating the existence of further modifications and a much more complex map of PTMs. An example is the recently discovered protein modification polyphosphorylation. Polyphosphorylation is mediated by inorganic polyphosphate (polyP) and represents the covalent attachment of this linear polymer of orthophosphate to lysine residues in target proteins. This modification has eluded MS analysis as both polyP itself and the phosphoramidate bonds created upon its reaction with lysine residues are highly unstable in acidic conditions. Polyphosphorylation detection was only possible through extensive biochemical characterization. Two targets have been identified: nuclear signal recognition 1 (Nsr1) and its interacting partner, topoisomerase 1 (Top1). Polyphosphorylation occurs within a conserved N-terminal polyacidic serine (S) and lysine (K) rich (PASK) cluster. It negatively regulates Nsr1–Top1 interaction and impairs Top1 enzymatic activity, namely relaxing supercoiled DNA. Modulation of cellular levels of polyP regulates Top1 activity by modifying its polyphosphorylation status. Here we discuss the significance of the recently identified new role of inorganic polyP.

scholarly journals A Novel Mutation in the AVPR2 Gene in a Palestinian Family with Nephrogenic Diabetes Insipidus

2017 ◽  
Vol 07 (01) ◽  
pp. e1-e3
Author(s):  
Abdulsalam Abu-Libdeh ◽  
Isaiah Wexler ◽  
Imad Dweikat ◽  
David Zangen ◽  
Bassam Abu-Libdeh
Keyword(s):  
Diabetes Insipidus ◽  
Nephrogenic Diabetes Insipidus ◽  
Novel Mutation ◽  
Collecting Duct ◽  
Failure To Thrive ◽  
Male Infant ◽  
Gene Encoding ◽  
Exon 2 ◽  
Recessive Form ◽  
V2 Vasopressin Receptor

AbstractNephrogenic diabetes insipidus (NDI) is a urinary concentrating defect resulting from resistance of the collecting duct to the antidiuretic action of vasopressin (AVP). The X-linked recessive form is the most frequent genetic cause of inherited NDI and can be caused by mutations in the gene encoding the V2 vasopressin receptor (AVPR2). A Palestinian male infant presented in the neonatal period with failure to thrive, vomiting, irritability, fever, and polyuria, and had biochemical findings consistent with NDI. The diagnosis of NDI was established based on the clinical picture, absent response to desmopressin, and a similarly affected elder brother. Sequencing of the AVPR2 gene for the patient and his affected brother revealed a novel missense mutation with replacement of G by A in codon 82 located in exon 2 (TGC → TAC), causing a cysteine to tyrosine substitution (C82Y). Testing of the mother showed that she was the carrier of that mutation. This is the identified AVPR2 mutation in a Palestinian family. Knowledge of these mutations will allow genetic counseling and early diagnosis of affected males.

scholarly journals Genetic Basis for Natural and Acquired Resistance to the Diarylquinoline R207910 in Mycobacteria

2006 ◽  
Vol 50 (8) ◽  
pp. 2853-2856 ◽  
Author(s):  
Stephanie Petrella ◽  
Emmanuelle Cambau ◽  
Aurelie Chauffour ◽  
Koen Andries ◽  
Vincent Jarlier ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Basis ◽  
Acquired Resistance ◽  
Natural Resistance ◽  
Mycobacterial Species ◽  
New Mutation ◽  
Gene Encoding ◽  
Mycobacterium Xenopi ◽  
Conserved Residue

ABSTRACT The atpE gene encoding the subunit c of the ATP synthase of Mycobacterium tuberculosis, the target of the new diarylquinoline drug R207910, has been sequenced from in vitro mutants resistant to the drug. The previously reported mutation A63P and a new mutation, I66M, were found. The genetic diversity of atpE in 13 mycobacterial species was also investigated, revealing that the region involved in resistance to R207910 is conserved, except in Mycobacterium xenopi in which the highly conserved residue Ala63 is replaced by Met, a modification that may be associated with the natural resistance of M. xenopi to R207910.

scholarly journals Spondyloocular Syndrome: A Novel XYLT2 Variant with Description of the Neonatal Phenotype

2021 ◽  
Vol 12 ◽  
Author(s):  
Gabriella Doddato ◽  
Alessandra Fabbiani ◽  
Chiara Fallerini ◽  
Mirella Bruttini ◽  
Theodora Hadjistilianou ◽  
...  
Keyword(s):  
Autosomal Recessive ◽  
Phenotypic Variability ◽  
Autosomal Recessive Inheritance ◽  
Nuchal Translucency ◽  
Gene Encoding ◽  
Nasal Bridge ◽  
Facial Profile ◽  
Pathogenic Variants ◽  
Skeletal Defects ◽  
Bone Abnormalities

Spondyloocular syndrome (SOS) is a skeletal disorder caused by pathogenic variants in XYLT2 gene encoding a xylotransferase involved in the biosynthesis of proteoglycans. This condition, with autosomal recessive inheritance, has a high phenotypic variability. It is characterized by bone abnormalities (osteoporosis, fractures), eye and cardiac defects, hearing impairment, and varying degrees of developmental delay. Until now only 20 mutated individuals have been reported worldwide. Here, we describe two siblings from consanguineous healthy parents in which a novel homozygous frameshift variant c.1586dup p(Thr530Hisfs*) in the XYLT2 gene was detected by exome sequencing (ES). The first patient (9 years) presented short stature with skeletal defects, long face, hearing loss and cataract. The second patient, evaluated at a few days of life, showed macrosomia, diffuse hypertrichosis on the back, overabundant skin in the retronucal area, flattened facial profile with drooping cheeks, elongated eyelid rims, wide and flattened nasal bridge and turned down corners of the mouth. During the prenatal period, high nuchal translucency and intestinal hyperechogenicity were observed at ultrasound. In conclusion, these two siblings with a novel pathogenic variant in XYLT2 further expand the clinical and mutational spectrum of SOS.

scholarly journals FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Christoph N Schlaffner ◽  
Konstantin Kahnert ◽  
Jan Muntel ◽  
Ruchi Chauhan ◽  
Bernhard Y Renard ◽  
...  
Keyword(s):  
Protein Modification ◽  
Large Scale ◽  
Software Tool ◽  
Label Free ◽  
Anaphase Promoting Complex ◽  
Proteomics Data ◽  
Single Experiment ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Modified Peptides

Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.

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