Biology subjects

Venugopal, A.

Publications and source records attributed to Venugopal, A..

6 recordsLinked to original sources

bioRxiv2025

OCRL regulates lysosomal function and endolysosomal homeostasis in Drosophila nephrocytes

The OCRL gene encodes a lipid phosphatase that dephosphorylates phosphatidylinositol 4,5 bisphosphate [(PI(4,5)P2]. Mutations in OCRL lead to a rare human genetic disorder, Lowe syndrome (LS) that affects the eye, kidney and brain. OCRL is widely expressed in cells and is localized to multiple organelles, including the plasma membrane, endosomes, Golgi and lysosomes. Although multiple defects in the endo-lysosomal system have been reported in OCRL depleted cells, the primary site of action of OCRL is unclear. Here we present a Drosophila nephrocyte model of LS; depletion of Drosophila OCRL (dOCRL) manifests with defects in endocytic uptake, altered endosomal compartments as well as expanded but dysfunctional lysosomes. Reconstitution of dOCRL depleted nephrocytes with a lysosome targeted version of the enzyme rescues not only the lysosomal defects but surprisingly also defects in endosomal structure and function. These findings suggest that the primary defect in LS cells is likely to be altered lysosome structure and function. Therefore, regulation of PI(4,5)P2 homeostasis at the lysosome membrane by OCRL is critical to homeostasis of the endosomal system.

cell biology↗

bioRxiv2025

Phosphatidylinositol 5 phosphate 4 kinase regulates phosphatidylinositol 3,4 bisphosphate levels in vivo.

In Drosophila, loss of phosphatidylinositol 5 phosphate 4 kinase (PIP4K) results in a reduction in larval salivary gland cell size. Previous studies have shown that this reduction in cell size is not correlated with the levels of phosphatidylinositol 5 phosphate (PI5P), the canonical substrate of PIP4K but to the levels of phosphatidylinositol 3 phosphate (PI3P) a substrate that is used less effectively by the PIP4K enzyme in vitro. The phosphorylation of PI3P by PIP4K generates phosphatidylinositol 3,4 bisphosphate [PI(3,4)P2]. Using a biosensor for PI(3,4)P2, surprisingly, we find that depletion of PIP4K leads to an elevation of intracellular PI(3,4)P2 punctae in salivary gland cells. This elevation in PI(3,4)P2 punctae was not dependent on the catalytic activity of dPIP4K. Rather, we found that the elevation of PI(3,4)P2 was dependent on the catalytic activity of Class II phosphatidylinositol 3 kinase (Class II PI3K). Thus, the PIP4K protein regulates an intracellular pool of PI(3,4)P2 via Class II PI3K activity in Drosophila cells.

cell biology↗

bioRxiv2024

Computational analysis of morphological changes in Lactiplantibacillus plantarum under acidic stress

Cell shape and size often define characteristics of individual or communities of microorganisms in changing environments. Hence, characterizing cell morphology using computational image analysis can aid in the accurate identification of bacterial responses to these changes. Modifications in cell morphology of Lactiplantibacillus plantarum were determined in response to acidic stress, specifically during growth stage of the cells at pH 3.5 compared to pH 6.5. Consequently, we developed a computational method to sort, detect, analyze, and measure bacterial size in a single-species culture. We applied a deep learning methodology composed of object detection followed by image classification to measure the bacterial cell dimensions of the pre-identified cells. The results of our computational analysis show a significant change in cell morphology in response to alteration of environmental pH. Specifically, we found that the cell was dramatically elongated at low pH, while the width was not altered. Those changes could be attributed to modifications in membrane properties, for instance increased cell membrane fluidity in acidic pH. Integration of deep learning with microbial microscopic imaging is an advanced methodology for studying cellular structures. These trained models and scripts can be applied to other microbes and cells and are publicly available at: https://github.com/OraMoyal26/bacteria_dimensions/tree/main

systems biology↗

bioRxiv2024

A genetic and physiological model of renal dysfunction in Lowe syndrome

Lowe syndrome (LS) is an X-linked recessive genetic disorder characterized by renal dysfunction, neurodevelopmental defects, and cataract. The affected gene, OCRL encodes for a polyphosphoinositide 5-phosphatase. OCRL is localized to multiple sub-cellular locations in the endolysosomal system and defects in these organelles have been described in human cells depleted of OCRL. However, the relationship of the endolysosomal defects in OCRL depleted cells to the altered physiology of kidney cells of LS patients has not been completely determined. Here we model the kidney phenotypes of LS using a Drosophila nephrocyte model. Using this model system, we demonstrate that OCRL plays a cell-autonomous role in nephrocyte function. Deletion of the only OCRL ortholog in Drosophila (dOCRL) leads to cell-autonomous defects in larval nephrocyte structure and function. Null mutants of dOCRL (dOCRLKO) show defects in the endolysosomal system of larval nephrocytes that are associated with physiological defects in nephrocyte function. These defects could be rescued by reconstitution with a human OCRL transgene but not with a phosphatase dead version or a human LS patient derived mutation. Overall, this work provides a model system to understand the mechanisms by which the sub-cellular changes from loss of OCRL leads to defects in kidney function in human patients.

cell biology↗

bioRxiv2022

PI3P dependent regulation of cell size by phosphatidylinositol 5-phosphate 4-kinase

Phosphatidylinositol 3-phosphate (PI3P) and Phosphatidylinositol 5-phosphate (PI5P) are low abundant phosphoinositides crucial for key cellular events such as endosomal trafficking and autophagy. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is an enzyme that regulates PI5P in vivo but can act on both PI5P and PI3P, in vitro. In this study, we report a novel role for PIP4K in regulating PI3P levels in Drosophila tissues. Loss-of-function mutants of the only PIP4K gene in Drosophila (dPIP4K29) show reduced cell size in larval salivary glands. We find that PI3P levels are elevated in dPIP4K29 tissues and that reverting PI3P levels back towards wild type, without changes in PI5P levels, can also rescue the reduced cell size phenotype. dPIP4K29 mutants also show an upregulation in autophagy and the reduced cell size can be reverted by decreasing Atg8a, that is required for autophagosome maturation. Lastly, increasing PI3P levels in wild type salivary glands can phenocopy the reduction in cell size and associated upregulation of autophagy seen in dPIP4K29. Thus, our study reports for the first time, a role for a PIP4K-regulated PI3P pool in the control of autophagy and cell size regulation that may explain the reported role of PIP4K in regulating neurodegeneration and tumour growth.

cell biology↗

bioRxiv2020

Lectins-glycoconjugates interactions: Experimental and computational docking studies of the binding and agglutination of eight different lectins in a comparative manner

Altering the lectin properties by chemically synthesized glycoconjugates is important in glycobiology. A series of eight plant lectins with varying carbohydrate specificity were chosen as model systems to study the binding by synthetic glycoconjugates. One of our earlier paper 1 deals with the binding of glycoconjugates by jacalin. Further to this, we have now extended the studies to several other lectins having specificities towards glucose/mannose, galactose and lactose, and the results are reported in this paper on a comparative manner. The binding aspects were established by hemagglutination and fluorescence spectroscopy, and the conformational changes by CD spectroscopy. Out of the fourteen glycoconjugates used in the present study, a galactosyl-naphthyl derivative, 1c turns out to be most effective towards galactose-specific lectin in agglutination inhibition, fluorescence quenching by inducing considerable conformational changes. Similarly, mannosyl-naphthyl derivative, 3c turns out to be most effective in inhibiting the agglutination of Glc/Man specific lectins. Present study demonstrates differential recognition of conjugates towards lectins. The results also supported the existence of a correlation between the glycoconjugate and lectin specificity at the carbohydrate recognition domain (CRD). The glycoconjugate that inhibits the agglutination binds in the CRD via polar interactions as well as by nonpolar/hydrophobic interactions arising from the aromatic moiety of the conjugate, whereas, the non-inhibiting conjugates bind primarily via hydrophobic interactions. The specific and selective binding of the glycoconjugates by these lectins were proven by the docking studies. Thus, the present study has contributed immensely towards understanding the molecular interactions present between the lectins and small molecules that will eventually help better drug design where the presence of hydrophoibic moieties would play important role.

biochemistry↗