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1.
Acta Neuropathol ; 146(2): 353-368, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37119330

RESUMO

Hereditary spastic paraplegias (HSP) are rare, inherited neurodegenerative or neurodevelopmental disorders that mainly present with lower limb spasticity and muscle weakness due to motor neuron dysfunction. Whole genome sequencing identified bi-allelic truncating variants in AMFR, encoding a RING-H2 finger E3 ubiquitin ligase anchored at the membrane of the endoplasmic reticulum (ER), in two previously genetically unexplained HSP-affected siblings. Subsequently, international collaboration recognized additional HSP-affected individuals with similar bi-allelic truncating AMFR variants, resulting in a cohort of 20 individuals from 8 unrelated, consanguineous families. Variants segregated with a phenotype of mainly pure but also complex HSP consisting of global developmental delay, mild intellectual disability, motor dysfunction, and progressive spasticity. Patient-derived fibroblasts, neural stem cells (NSCs), and in vivo zebrafish modeling were used to investigate pathomechanisms, including initial preclinical therapy assessment. The absence of AMFR disturbs lipid homeostasis, causing lipid droplet accumulation in NSCs and patient-derived fibroblasts which is rescued upon AMFR re-expression. Electron microscopy indicates ER morphology alterations in the absence of AMFR. Similar findings are seen in amfra-/- zebrafish larvae, in addition to altered touch-evoked escape response and defects in motor neuron branching, phenocopying the HSP observed in patients. Interestingly, administration of FDA-approved statins improves touch-evoked escape response and motor neuron branching defects in amfra-/- zebrafish larvae, suggesting potential therapeutic implications. Our genetic and functional studies identify bi-allelic truncating variants in AMFR as a cause of a novel autosomal recessive HSP by altering lipid metabolism, which may potentially be therapeutically modulated using precision medicine with statins.


Assuntos
Inibidores de Hidroximetilglutaril-CoA Redutases , Paraplegia Espástica Hereditária , Animais , Humanos , Paraplegia Espástica Hereditária/tratamento farmacológico , Paraplegia Espástica Hereditária/genética , Inibidores de Hidroximetilglutaril-CoA Redutases/farmacologia , Inibidores de Hidroximetilglutaril-CoA Redutases/uso terapêutico , Peixe-Zebra , Mutação , Neurônios Motores , Receptores do Fator Autócrino de Motilidade/genética
2.
Bioinformatics ; 36(3): 948-949, 2020 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-31392322

RESUMO

MOTIVATION: In vivo protein folding is governed by molecular chaperones, that escort proteins from their translational birth to their proteolytic degradation. In E.coli the main classes of chaperones that interact with the nascent chain are trigger factor, DnaK/J and GroEL/ES and several authors have performed whole-genome experiments to construct exhaustive client lists for each of these. RESULTS: We constructed a database collecting all publicly available data of experimental chaperone-interaction and -dependency data for the E.coli proteome, and enriched it with an extensive set of protein-specific as well as cell context-dependent proteostatic parameters. We made this publicly accessible via a web interface that allows to search for proteins or chaperone client lists, but also to profile user-specified datasets against all the collected parameters. We hope this will accelerate research in this field by quickly identifying differentiating features in datasets. AVAILABILITY AND IMPLEMENTATION: The Protein Homeostasis Database is freely available without any registration requirement at http://PHDB.switchlab.org/.


Assuntos
Proteínas de Escherichia coli , Escherichia coli , Proteínas de Choque Térmico HSP70 , Chaperonas Moleculares , Dobramento de Proteína , Proteostase
3.
Genet Med ; 23(11): 2122-2137, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34345025

RESUMO

PURPOSE: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. METHODS: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. RESULTS: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. CONCLUSION: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.


Assuntos
Epilepsia , Histona-Lisina N-Metiltransferase , Deficiência Intelectual , Transtornos do Neurodesenvolvimento , Epilepsia/diagnóstico , Epilepsia/genética , Histona-Lisina N-Metiltransferase/genética , Humanos , Deficiência Intelectual/diagnóstico , Deficiência Intelectual/genética , Masculino , Transtornos do Neurodesenvolvimento/diagnóstico , Transtornos do Neurodesenvolvimento/genética , Fenótipo , Convulsões/diagnóstico , Convulsões/genética
4.
Bioinformatics ; 35(20): 4098-4107, 2019 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-30903148

RESUMO

MOTIVATION: Despite intense effort, it has been difficult to explain chaperone dependencies of proteins from sequence or structural properties. RESULTS: We constructed a database collecting all publicly available data of experimental chaperone interaction and dependency data for the Escherichia coli proteome, and enriched it with an extensive set of protein-specific as well as cell-context-dependent proteostatic parameters. Employing this new resource, we performed a comprehensive meta-analysis of the key determinants of chaperone interaction. Our study confirms that GroEL client proteins are biased toward insoluble proteins of low abundance, but for client proteins of the Trigger Factor/DnaK axis, we instead find that cellular parameters such as high protein abundance, translational efficiency and mRNA turnover are key determinants. We experimentally confirmed the finding that chaperone dependence is a function of translation rate and not protein-intrinsic parameters by tuning chaperone dependence of Green Fluorescent Protein (GFP) in E.coli by synonymous mutations only. The juxtaposition of both protein-intrinsic and cell-contextual chaperone triage mechanisms explains how the E.coli proteome achieves combining reliable production of abundant and conserved proteins, while also enabling the evolution of diverging metabolic functions. AVAILABILITY AND IMPLEMENTATION: The database will be made available via http://phdb.switchlab.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Proteínas de Escherichia coli/metabolismo , Chaperonina 60 , Escherichia coli , Proteínas de Choque Térmico HSP70 , Chaperonas Moleculares
5.
Microb Cell Fact ; 17(1): 43, 2018 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-29544487

RESUMO

BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible. We first introduced a uniform, improved nomenclature that re-annotated the names of ~ 4000 proteins based on functional and structural information. Then protein localization was assigned de novo using prediction tools and edited by manual curation for 7494 proteins, including information for 183 proteins that resulted from a recent genome re-annotation and are not available in current databases. The S. lividans proteome was also linked with those of other model bacterial strains including Streptomyces coelicolor A3(2) and Escherichia coli K-12, based on protein homology, and can be accessed through an open web interface. Finally, experimental data derived from proteomics experiments have been incorporated and provide validation for protein existence or topology for 579 proteins. Proteomics also reveals proteins released from vesicles that bleb off the membrane. All export systems known in S. lividans are also presented and exported proteins assigned export routes, where known. CONCLUSIONS: SToPSdb provides an updated and comprehensive protein localization annotation resource for S. lividans and other streptomycetes. It forms the basis for future linking to databases containing experimental data of proteomics, genomics and metabolomics studies for this organism.


Assuntos
Peptídeos/metabolismo , Proteômica/métodos , Streptomyces/genética
6.
Parkinsonism Relat Disord ; 108: 105323, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36805523

RESUMO

BACKGROUND: Phosphodiesterase 10A (PDE10A) controls body movements by regulating cyclic adenosine monophosphate signaling in the basal ganglia. Two classes of PDE10A variants are reported with distinctive genotype-phenotype correlation. The autosomal recessive mutations in the GAF-A and catalytic domains are associated with compromised membrane localization, and manifest with infantile onset chorea, developmental, and cognition delay with normal brain MRI. Conversely, autosomal dominant mutations in the GAF-B domain cause protein aggregates which results in childhood onset chorea in the context of normal cognition and development, with striatal lesions. METHODS: Phenotypic characteristics of affected individuals with PDE10A mutations belonging to a single family were recorded. In addition, Sanger sequencing and in silico analysis were used to identify the mutations. Homozygosity mapping was applied together with whole exome sequencing. RESULTS: Four individuals from a consanguineous family affected with PDE10A mutations were observed for up to 40 years. Although these individuals displayed a clinical phenotype attributed to the recessive GAF-A mutations, they revealed a bi-allelic GAF-B mutation (c.883G > A:p. D295 N; p.Asp295Asn) that was segregated with all affected individuals. In addition to chorea, we observed peculiar foot deformities and pronounced social phobia, with normal brain MRI. In silico structural analysis suggested that the GAF-B mutation blocked allosteric PDE10A activation. The resulting lack of PDE10A activity likely phenocopies GAF-A mutations, and this is achieved through a distinct mechanism. CONCLUSIONS: Collectively, our findings demonstrate the association of recessive and dominant phenotypes of known variants, and further expands the genotype-phenotype landscape of PDE10A-associated movement disorders.


Assuntos
Coreia , Transtornos dos Movimentos , Humanos , Coreia/genética , Diester Fosfórico Hidrolases/genética , Genótipo , Fenótipo
7.
Front Pediatr ; 9: 582816, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33937142

RESUMO

Background: Craniosynostosis (CS) is defined as pre-mature fusion of one or more of the cranial sutures. CS is classified surgically as either simple or complex based on the number of cranial sutures involved. CS can also be classified genetically as isolated CS or syndromic CS if the patient has extracranial deformities. Currently, the link between clinical and genetic patterns of CS in the Saudi population is poorly understood. Methodology: We conducted a retrospective cohort study among 28 CS patients, of which 24 were operated and four were not. Clinical and genetic data were collected between February 2015 and February 2019, from consenting patient's families. The electronic chart data were collected and analyzed including patient demographics, craniofacial features, other anomalies and dysmorphic features, operative data, intra cranial pressure (ICP), parent consanguinity and genetic testing results. Results: The most common deformity in our population was trigonocephaly. The most performed procedure was cranial vault reconstruction with fronto-orbital advancement, followed by posterior vault distraction osteogenesis and suturectomy with barrel staving. Genetics analysis revealed pathogenic mutations in FGFR2 (6 cases), TWIST1 (3 cases), ALPL (2 cases), and TCF12 (2 cases), and FREM1 (2 case). Conclusion: Compared to Western countries, our Saudi cohort displays significant differences in the prevalence of CS features, such as the types of sutures and prevalence of inherited CS. The genomic background allows our phenotype-genotype study to reclassify variants of unknown significance. Worldwide, the sagittal suture is the most commonly affected suture in simple CS, but in the Saudi population, the metopic suture fusion was most commonly seen in our clinic. Further studies are needed to investigate the characteristics of CS in our population in a multicenter setting.

8.
Front Microbiol ; 10: 1670, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31404336

RESUMO

Cellular proteomes are distributed in multiple compartments: on DNA, ribosomes, on and inside membranes, or they become secreted. Structural properties that allow polypeptides to occupy subcellular niches, particularly to after crossing membranes, remain unclear. We compared intrinsic and extrinsic features in cytoplasmic and secreted polypeptides of the Escherichia coli K-12 proteome. Structural features between the cytoplasmome and secretome are sharply distinct, such that a signal peptide-agnostic machine learning tool distinguishes cytoplasmic from secreted proteins with 95.5% success. Cytoplasmic polypeptides are enriched in aliphatic, aromatic, charged and hydrophobic residues, unique folds and higher early folding propensities. Secretory polypeptides are enriched in polar/small amino acids, ß folds, have higher backbone dynamics, higher disorder and contact order and are more often intrinsically disordered. These non-random distributions and experimental evidence imply that evolutionary pressure selected enhanced secretome flexibility, slow folding and looser structures, placing the secretome in a distinct protein class. These adaptations protect the secretome from premature folding during its cytoplasmic transit, optimize its lipid bilayer crossing and allowed it to acquire cell envelope specific chemistries. The latter may favor promiscuous multi-ligand binding, sensing of stress and cell envelope structure changes. In conclusion, enhanced flexibility, slow folding, looser structures and unique folds differentiate the secretome from the cytoplasmome. These findings have wide implications on the structural diversity and evolution of modern proteomes and the protein folding problem.

9.
Nat Commun ; 9(1): 866, 2018 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-29491361

RESUMO

Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichia coli and Acinetobacter baumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy.


Assuntos
Acinetobacter baumannii/metabolismo , Proteínas de Bactérias/química , Escherichia coli/metabolismo , Proteoma/química , Proteostase , Acinetobacter baumannii/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Escherichia coli/genética , Agregados Proteicos , Dobramento de Proteína , Proteoma/genética , Proteoma/metabolismo
10.
Mater Sci Eng C Mater Biol Appl ; 61: 631-7, 2016 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-26838891

RESUMO

Cellulose pulp has a visible market share in personal hygiene products such as sanitary napkins and baby diapers. However it offers good surface for growth of microorganisms. Huge amount of research is going on in developing hygiene products that do not initiate microbial growth. The objective of the present work is to produce antibacterial cellulose pulp by depositing silver nanopowder on the cellulose fiber. The silver nanoparticles used were of less than 100 nm in size and were characterised using transmission electron microscopy and X-ray powder diffraction studies. Antibacterial activity of the functionalized cellulose pulp was proved by JIS L 1902 method. The in-vitro cytotoxicity, in-vivo vaginal irritation and intracutaneous reactivity studies were done with silver nanopowder incorporated cellulose pulp for introducing a new value added product to the market. Cytotoxicity evaluation suggested that the silver nanoparticle incorporated cellulose pulp is non-cytotoxic. No irritation and skin sensitization were identified in animals tested with specific extracts prepared from the test material in the in-vivo experiments. The results indicated that the silver nanopowder incorporated cellulose pulp meets the requirements of the standard practices recommended for evaluating the biological reactivity and has good biocompatibility, hence can be classified as a safe hygiene product.


Assuntos
Celulose , Teste de Materiais , Nanopartículas Metálicas/química , Prata , Animais , Linhagem Celular , Celulose/química , Celulose/farmacologia , Feminino , Higiene , Masculino , Camundongos , Coelhos , Prata/química , Prata/farmacologia
11.
Contraception ; 92(6): 585-8, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26363430

RESUMO

BACKGROUND: The adverse effects of copper intrauterine devices (IUDs) such as abnormal bleeding, pain and cramps may be due in part to the burst release of copper ions during the first few months of usage. This study focuses on controlling the initial burst release of copper ions. STUDY DESIGN: This study evaluated in vitro release rates of copper for a period of 1 year from standard CuT380 IUDs (n=6) and from CuT380 IUDs coated with poly(dl-lactide-co-glycolide) (PLGA) films (n=6). This study characterized the coated device for its morphological changes during degradation of film by scanning electron microscopy (SEM). RESULTS: CuT380 IUDs coated with PLGA film with a thickness of 0.10±0.02 mm showed a reduced initial copper release (40-80 mcg/day) compared with uncoated CuT380 IUDs (150-200 mcg/day). Statistically significant (p<.05) results were obtained at different time intervals during the overall study period of 1 year. SEM images showed degradation of coating. CONCLUSION: Coating a CuT380 IUD with biodegradable polymer reduced the initial copper release without affecting release at 1 year. Clinical trials are required to determine whether this could reduce side effects such as bleeding and pain associated with copper containing IUDs.


Assuntos
Cobre/análise , Desenho de Equipamento/métodos , Dispositivos Intrauterinos de Cobre/efeitos adversos , Polímeros/metabolismo , Oligoelementos/análise , Feminino , Humanos , Microscopia Eletrônica de Varredura , Poliglactina 910/uso terapêutico
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