Biology subjects

Rangasamy, S.

Publications and source records attributed to Rangasamy, S..

6 recordsLinked to original sources

bioRxiv2025

Extraordinary activation of CALB by alkylammonium ions: a new paradigm for activity enhancement of enzymes

Candida antarctica lipase B (CALB) is widely used in biocatalysis with applications in plastics degradation and chemical synthesis. CALB is activated by hydrophobic matrices and, enigmatically, shows striking activation in polar, choline-based, Deep Eutectic Solvents (DES). Herein, we show that CALB activation and stabilisation by TAAs is caused by binding to cholines tetraalkylammonium (TAA) moiety. Several related TAA salts also caused CALB activation which was proportional to the hydrophobicity of their alkyl substituents. Remarkably, tetraoctylammonium bromide showed activation of [~]500% even at low micromolar levels. These TAA salts represent a new class of enzyme activator. Molecular modelling identified the alkylammonium binding location as a hydrophobic patch centred around Asp-145 of CALB. Binding at this site explains lipase activation in polar DES solvents and its relationship to other pathways of CALB activation. Herein, we also demonstrate that CALB, like many lipases, is activated by calcium. Intriguingly, mixed soluble activator experiments showed that calcium and choline bind to different CALB sites, suggesting a two-site model for CALB activation. These observations, along with previous findings, show that TAA activation is a widespread property of enzymes and constitutes a novel and potent means to enhance enzyme turnover and stability. HighlightsO_LICALB is activated by choline C_LIO_LISeveral tetraalkylammonium salts cause activation of CALB C_LIO_LIHyperactivation of CALB (5-fold) by tetraoctylammonium ions occurs at low micromolar concentrations. C_LIO_LITwo independent sites for CALB activation, by calcium and TAA ions, are identified C_LIO_LIActivation at the choline binding site stabilises CALB while calcium binding destabilises the enzyme C_LIO_LIA soluble activator is demonstrated, that can be used to probe the activation mechanism of CALB or other enzymes. C_LI

bioengineering↗

bioRxiv2024

Characterizing CSNK2A1 Mutant-Induced Morphological Phenotypes in Zebrafish (Danio rerio): Insights into Okur-Chung Neurodevelopmental Syndrome (OCNDS)

Okur-Chung Neurodevelopmental Syndrome (OCNDS) is a rare, autosomal dominant disorder caused by heterozygous pathogenic variants in the CSNK2A1 gene. CSNK2A1 encodes the subunit of protein kinase CK2, involved in diverse biological processes. In 2016, Okur et al. reported the discovery of germline de novo missense and canonical splice site mutations in CSNK2A1 in five female patients with OCNDS. The syndrome is characterized by developmental delays, intellectual disability, hypotonia, feeding difficulties, dysmorphic facial features, and disrupted circadian rhythms, leading to sleep disturbances. The complex phenotypic spectrum of OCNDS underscores the need for robust model systems to investigate genotype-phenotype correlations, disease mechanisms, and potential therapies. In this study, we employed an overexpression strategy in a zebrafish model to investigate the functional consequences of select CSNK2A1 variants implicated in OCNDS. Our findings revealed distinct morphological phenotypes resulting from the overexpression of different CSNK2A1 mutants, indicating a direct correlation between genetic alterations and phenotypic manifestations. Notably, the CSNK2A1 p.Arg191Ter (R191X) mutation had a significant impact on the phenotype. Co-injection of wild-type CSNK2A1 mRNA with mutant CSNK2A1 mRNA rescued morphological abnormalities in zebrafish embryos. Overall our study highlights the utility of zebrafish as an adaptable model system for examining the functional impact of CSNK2A1 mutations and exploring novel therapeutic avenues.

neuroscience↗

bioRxiv2023

From mice to humans: Cross-species transcriptomics analysis to uncover distinct mechanisms of Diabetic Retinopathy (DR)

Diabetic Retinopathy (DR) is the leading risk for vision loss in working adults worldwide, affecting more than 100 million people. While risk factors such as diabetes duration, hyperglycemia, and dyslipidemia are well-acknowledged, the unifying molecular mechanisms underlying the pathogenesis of DR remain incompletely understood across different species. To bridge this gap, we conducted a comprehensive RNA-sequencing (RNA-seq) meta-analysis on retinal tissue samples from mice, rats, and humans with diabetes. Our integrative bioinformatics analysis elucidated both conserved and species-specific transcriptional landscapes associated with DR. Notably, pro-inflammatory pathways were ubiquitously activated in the retinal tissues across all examined species. However, unique human-specific immune-metabolic signatures emerged, which were not observed in rodent models. In summary, our investigation unveils both universal and species-specific molecular underpinnings of DR, enhancing our understanding of its complex pathobiology. These findings validate the utility of animal models in DR research and underscore the importance of human-focused studies to uncover mechanisms uniquely relevant to human pathology.

pathology↗

bioRxiv2021

Pathological LSD1 mutations cause HDAC-mediated aberrant gene repression during early cell differentiation

Lysine-specific demethylase 1 (LSD1/KDM1A) demethylates both histone and non-histone substrates, recruits repressive chromatin complexes, and is increased in cancers. De novo LSD1 mutations impairing protein function lead to a rare developmental disorder, but the molecular details of the pathology remains unclear. Using patient-derived fibroblasts, reprogrammed pluripotent stem cells, and differentiated cells, we found over 4000 differentially expressed genes and 68 transcription factors (TFs) whose motif accessibilities changed upon LSD1 mutation. An enhancer-mediated gene regulatory network approach identified transcriptional repressors with impaired activity in fibroblast and stem cells, leading to erroneous activation of their target genes. We also revealed overall decreases in TF target gene expression during early lineage differentiation of LSD1 mutant stem cells, likely caused by increased activity of repressive histone deacetylases (HDACs), co-factors of LSD1. Indeed, an HDACs inhibitor restored changes in gene expression including downregulation phenotype. Our findings characterize the molecular pathogenesis of LSD1 mutations and suggest potential therapeutic strategies for the developmental disorder and cancers caused by LSD1 dysregulations.

genomics↗

bioRxiv2020

Bisbee: A proteomics validated analysis package for detecting differential splicing, identifying splice outliers, and predicting splice event protein effects

Here we present a novel statistical approach to splicing outlier and differential splicing detection, implemented in a software package called Bisbee. We leverage Bisbees prediction of protein level effects to benchmark using matched RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches. We applied Bisbee to confirm a pathogenic splicing event in a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic splice factor mutation. We also identified common tumor associated splice isoforms replicated in an independent dataset, demonstrating the utility of Bisbee in discovering disease relevant splice variants.

bioinformatics↗

bioRxiv2020

Complex genetic network underlying the convergent of Rett Syndrome like (RTT-L) phenotype in neurodevelopmental disorders

Mutations of the X-linked gene encoding methyl-CpG-binding protein 2 (MECP2) cause classical forms of Rett syndrome (RTT) in girls. Patients with features of classical Rett syndrome, but do not fulfill all the diagnostic criteria (e.g. absence of a MECP2 mutation), are defined as atypical Rett syndrome. Genes encoding for cyclin-dependent kinase-like 5 (CDKL5) and forkhead box G1 (FOXG1) are more commonly found in patients with atypical Rett syndrome. Nevertheless, a subset of patients who are recognized to have an overlapping phenotype with RTT but are lacking a mutation in a gene that causes typical or atypical RTT are described as having Rett syndrome like phenotype (RTT-L). Whole Exome Sequencing (WES) of 8 RTT-L patients from our cohort revealed mutations in the genes GABRG2, GRIN1, ATP1A2, KCNQ2, KCNB1, TCF4, SEMA6B, and GRIN2A, which are seemingly unrelated to Rett syndrome genes. We hypothesized that the phenotypic overlap in RTT and RTT-L is caused by mutations in genes that affect common cellular pathways critical for normal brain development and function. We annotated the list of genes identified causing RTT-L from peer-reviewed articles and performed a protein-protein interaction (PPI) network analysis. We also investigated their interaction with RTT (typical or atypical) genes such as MECP2, CDKL5, NTNG1, and FOXG1. We found that the RTT-L-causing genes were enriched in the biological pathways such as circadian entrainment, the CREB pathway, and RET signaling, and neuronal processes like ion transport, synaptic transmission, and transcription. We conclude that genes that significantly interact with the PPI network established by RTT genes cause RTT-L, explaining the considerable feature overlap between genes that are indicated for RTT-L and RTT.

genomics↗